Use and Resistance in Pigs and Chickens A review of the science, policy, and control practices from farm to slaughter

Prepared by:

Rosengren Consulting Ltd. Leigh Rosengren Sheryl Gow Scott Weese

With contribution from: Jamie Sofoifa Ashley Spencer Cheryl Waldner

November 2009 Antimicrobial Use and Resistance in Pigs and Chickens A review of the science, policy, and control practices from farm to slaughter Leigh B. Rosengren1, Sheryl P. Gow2, J. Scott Weese3 1 Rosengren Epidemiology Consulting Ltd., 2 Public Health Agency of Canada, 3 University of Guelph

general and resistant bacterial in particular. Executive Summary By broadening on farm food safety knowledge, policy Over the course of a century, have and interventions can expand from a specific focus on evolved from the panacea for bacterial infections AMU and AMR to improving overall food safety. to an endangered tool because of rising resistance. Resistant bacteria in animals are one source of Antimicrobials are a necessary tool for appropriate (AMR) for people and veterinary care of food animals. Certainly some AMU Canadians’ strongest connection to animals is our could be dispensed with while still humanely raising daily food. This report summarizes and evaluates the animals; but the data distinguishing why antimicrobials scientific knowledge and pertinent policy around the are used, and their range of effects, are limited world on AMR and antimicrobial use (AMU) in pigs so evaluating the appropriateness of agricultural and chickens. This document will serve as a reference AMU is contentious. For example, AMU to improve document for public heath, regulatory, and agricultural productivity is not necessary for good animal welfare policy makers and will hopefully initiate intense yet prophylactic and metaphylactic use arguably discussion among and between these groups. Public could be. The agriculture industry and regulators must health practitioners may find it informative regarding continue to address this problem together so that AMU notable AMR risks to the Canadian population related policy can preserve appropriate AMU, thus ensuring to food and agriculture. Key research and policy gaps the production of safe food and humane rearing of have been identified that compromise our ability to livestock, while eliminating inappropriate AMU practices control this problem. but still ensuring economic viability of the industry.

It is irrefutable that people can acquire antimicrobial Indisputably, AMU causes AMR. Yet, it is equally resistant bacteria from animals through food. What indisputable that the relationship is complex. Use remains unclear is the frequency that pathogenic and of some antimicrobials in some species in certain commensal bacteria are transmitted to humans and situations clearly results in resistance in some either cause disease or transfer resistance elements bacteria. However, what happens with one animal to bacteria in people. A related knowledge gap is the species, bacterium, antimicrobial, or management relative amounts that AMU in animals and humans system does not necessarily happen in others. each contribute to AMR in humans. Future research Evidence showing increasing resistance with should expand on both ends of the current farm-to- increasing AMU is far more consistent than evidence fork research continuum. This could be achieved by showing declining resistance with cessation of use. studying health outcomes caused by resistant bacteria, Our understanding is rudimentary of the complex and at the other end investigating why producers, selective pressures for resistance in livestock, the AMR nutritionists, and veterinarians use antimicrobials and rates between animals and people, and the factors that influence their decisions. This research the management practices that help or hinder the should be coupled with studies evaluating how emergence and persistence of resistance on farms. various on farm practices, only one of which is AMU, Such knowledge gaps make evaluating the risk posed affect the rate and severity of foodborne diseases in by AMU in livestock to public health a topic ripe for

i national collaborating centre for infectious diseases debate. Consequently, evidence-based interventions the slaughter and meat processing industry has are elusive and controversial. made substantial advancements in reducing bacterial contamination of meat. In North America, the rate Links through travel and trade make AMR in people of foodborne diseases declined after slaughter and and animals a global problem. International agencies processing plants implementing hazard analysis are supporting national solutions to this worldwide and critical control point (HACCP) systems. These issue through prudent AMU guidelines, surveillance interventions undoubtedly decreased the burden of strategies and standardized risk assessment illness in people from resistant bacteria in food but techniques. At home, Canada operates an integrated have not been quantified as our surveillance ends at AMU and AMR surveillance program in humans and ‘the fork,’ rather with than health outcomes. the major meat commodities. This program, along with an active research community, is providing Although great progress has been made, there government and industry strategists with a scientific is still a great deal of work to be completed. We foundation for decisions. Scrutiny of our veterinary have advocated for continued research but also drug regulations has resulted in preliminary policy recognize that such research is ineffective without and regulatory changes to eliminate inappropriate improvements in knowledge management. Novel antimicrobial access and use, but this process has techniques must be found to systematically assimilate been slow and leaves much to be done. The Canadian the immense volume of discrepant research, ensure government is responsible for ensuring the health of results are evaluated in context, and distribute the Canadians through policies and regulations that ensure contextualized output to practitioners and policy safe food production. It must carry this responsibility makers. Beyond this, the main recommendations out while concurrently supporting a sustainable from this report are as follows: livestock industry that can produce food in a financially and environmentally sound manner. This task requires • Seek and support research into the effectiveness continued commitment to evidence‑based policy and of interventions, including but not limited to AMU advocating that other nations do the same. withdrawal, to mitigate existing AMR

Without doubt, unnecessary and inappropriate AMU • Seek and support research that expands on the occurs in agriculture. There is currently no prudent current ‘farm-to-fork’ approach to account for AMU education for producers or nutritionists. Education diverse human health outcomes is desperately needed for the people who initiate • Advocate for fair, transparent, veterinary drug much of the agricultural AMU in Canada. Yet concerns regulations, AMR and AMU monitoring around the over inappropriate AMU often overshadow the good- world based on scientific evidence, risk assessment, news stories in the industry. Agriculture and veterinary and appropriate precaution to ensure free and have made advancements in animal health open trade of safe meat products that decrease their reliance on antimicrobials. Livestock producers have embraced improvements in sanitation, • Change Canada’s veterinary drug regulations to nutrition, and vaccine technology. Biosecurity enables ensure prudent and safe AMU while committing to flocks and herds to remain negative for diseases transparent policy evaluation that are in the industry—diseases that were traditionally controlled with antimicrobials. Producer- • Deliver antimicrobial use education to producers organizations have taken a proactive stance on food and nutritionists safety. Both chicken and pork have self-mandated on- • Foster an innovative and collaborative relationship farm food safety programs. These programs support between regulators, public health officials and the best management practices and appropriate AMU. agriculture industry In conjunction with these farm-based improvements,

www.nccid.ca ii Table of Contents Executive Summary...... i Introduction...... 1 Methods...... 3 Chapter 1: The Hazard of Antimicrobial Resistance in Foodborne Bacteria...... 6 Introduction to AMR Ecology...... 7 AMR in Foodborne Bacteria ...... 10 Zoonotic Bacteria ...... 10 Commensal Bacteria...... 14 Bacteria of Secondary Interest...... 18 Emerging Issues...... 20 Chapter 2: Antimicrobial Use...... 24 General Considerations, Terminology, and Reasons for Antimicrobial Use...... 25 Antimicrobial Use Estimates in Livestock Production ...... 28 Antimicrobial Use: Routes, Antimicrobials, and Reasons for Use...... 31 Relationship between Antimicrobial Use in Swine or Poultry and Antimicrobial Resistance...... 33 Information Gaps and Challenges in Understanding the Effects of Antimicrobial Use in Livestock on Public Health...... 36 Chapter 3: Overview of Antimicrobial Resistance Surveillance or Monitoring Programs and Subsequent Policy Outcomes...... 41 International Organizations’ Response to AMR in Agriculture...... 41 Policies, Strategy, Regulation, and Legislation to Address AMR in Agri-food...... 44 Surveillance and Monitoring of Antimicrobial Resistance and Use...... 51 Chapter 4: Agricultural and Agri-Food Interventions to Reduce the Impact of AMR Bacteria in Pigs and Chickens on Human Health...... 61 Chicken and Pig Production and the Broiler and Swine Industries...... 61 HACCP: On the Farm and At Slaughter...... 63 On-Farm Food Safety Program ������������������������������������������������������������������������������������������������������������������������������ 64 Prudent Antimicrobial Use Guidelines...... 65 Alternatives to Antimicrobials...... 66 Best Management Practices...... 70 Slaughter and Processing...... 73 Chapter 5: Conclusion...... 77 Main Recommendations and Knowledge Needs...... 82 References...... 83 Appendix 1: Search Strategy...... 111

iii national collaborating centre for infectious diseases Introduction

Arguably, one of the most important discoveries in rather unpredictable biological variation, indicating the medicine was the development of antimicrobials. need for detailed interdisciplinary (and international) It was not until the start of the ‘ era’ that study to optimally address this pressing issue. human and veterinary medicine became equipped to deal successfully with various bacterial diseases. The Antimicrobial use in animals and subsequent introduction of antimicrobials had profound effects identification of AMR in pathogens and commensal on patient morbidity and mortality and ushered in bacteria has raised numerous concerns. The greatest an era of great optimism. The optimism was so great involves the potential for AMU in animals to be that in 1967, the U.S. Surgeon General somewhat reflected in AMR in human pathogens. The closest infamously declared that it was “time to close the contact that most people have with livestock is book on infectious diseases” (1). In hindsight, through handling and consumption of food, and that statements such as that seem ludicrous as the is generally the main route of exposure of humans to pendulum has now swung in the opposite direction. bacteria of food-animal origin. As AMR increases in Some people have expressed concern that the end animals, and resistant bacteria contaminate food, the of the ‘antibiotic era’ may be near and questioned potential for human exposure increases. However, whether continued emergence of multidrug-resistant just as AMU can lead to AMR, and the presence of pathogens represents an ‘unwinnable war’ (2,3). Like resistant bacteria in animals can lead to infections most situations, the reality likely lies between those in people, defining what ‘can’ represents in terms of two extremes, but concerns over the emergence and true and risk is problematic. More objective dissemination of antimicrobial resistant pathogens in information is needed to quantify the health risk human and veterinary medicine are significant. and to develop interventions for the transmission of resistant bacteria to humans through food. It was not long after antimicrobials became widely used in human medicine that antimicrobial resistance A broad, multidisciplinary approach is needed to emerged in human pathogens. Biologically, there was address the relationships between AMU and AMR no reason to believe that the response of bacteria because this topic is constantly evolving with respect in livestock to antimicrobial exposure would be any to management practices, AMU, pathogen distribution, different and, indeed, the use of antimicrobials in monitoring methods, and research techniques. animals has certainly led to the development and This document provides an overview of issues, dissemination of AMR in various animal pathogens concerns, research, policies, regulations, strategies, and commensal organisms. It is irrefutable that and legislations pertaining to AMU and AMR in swine antimicrobial use (AMU) is a key component for and poultry, as well as an assessment of critical gaps development of antimicrobial resistance (AMR). in knowledge and efforts. Using a review and critical However, it is equally clear that there is not a simple assessment of the literature for relevant research, and consistent relationship between AMU and AMR. policies and strategies that can, or have been used Use of some antimicrobials in some species in certain to address AMR in swine and poultry, along with situations clearly results in resistance in some bacteria. consultation of relevant experts, this document takes However, something that happens with one animal a stepwise approach to understanding and assessing species, bacterium, drug, or management system this topic. The first step is a basic description of AMR does not necessarily happen in all others, illustrating ecology, including mechanisms of resistance and the complexity of the field. Responses to previous means of acquisition or transmission of resistance, in efforts to control AMR based solely on AMU have met order to provide the scientific background required for with variable responses because of this complex and assessment of this field. An understanding of zoonotic

www.nccid.ca 1 pathogens of particular concern with respect to AMU developed various approaches to reduce the impact and AMR in swine and in poultry is critical, but so is of AMR in chickens and pigs on human health. Key recognition of the role of the commensal microflora in interventions are highlighted. Potential therapies such AMR acquisition and transmission. Zoonotic bacteria of as prebiotics and probiotics are attractive but are lesser concern are also discussed, as is the potential largely unproven and under-investigated. Management role of some emerging pathogens that may become a measures to reduce the need for antimicrobials significant concern to the swine and poultry industries. through improved animal health are an obvious area of interest. Management can have a tremendous An understanding of current and historical effect on animal health, but research in many aspects antimicrobial use practices in livestock is provided, is limited and a broad approach balancing animal including why antimicrobials are used and how they health, animal welfare and production economics are administered. The strength of evidence on the is needed, thereby complicating this area. Research appropriateness of AMU in livestock production is on these topics is evaluated and presented with a evaluated. The logical extension of this is the merging description of the current production, management of the two initial topics, and an assessment of links and marketing system differences between swine between AMU and AMR in poultry and swine. An and poultry that can have an effect on feasibility, important aspect of this topic is critical assessment outcomes, and required measures. Additionally, of the current literature to address the contentious current AMU guidelines that have been developed question of the extent that AMU in swine and poultry are discussed in terms of their content, practical contributes to AMR in human pathogens. application and potential consequences.

Various policies, regulations, and legislations have Zoonotic diseases will certainly remain as a pressing been developed or enacted in an attempt to control concern in human medicine, and animal diseases AMU and AMR, with varying degrees of evidence and will be similarly important in veterinary medicine. efficacy. The complexity of the field, differences in Balancing human and animal health is a complex perspectives and absence of objective data in many concept as measures taken in one group can have key areas have led to much controversy regarding unpredictable or unknown effects in the other. Clearly, previous, current, and proposed control methods. there are no straightforward answers for control of this The various organizations involved in AMU and issue. Cessation of all antimicrobial use is not practical AMR and their roles are described. This includes for animal health, animal welfare, and production both international bodies and national systems. economics. Continuation of the status quo is similarly Additionally, the surveillance activities of these groups unacceptable because of evidence regarding the are compared. The varied approaches between groups impact of agricultural AMU on some aspects of human underlie the differences in concern, perceptions, disease. Identification of the appropriate middle resources, and leadership in different countries and ground is required to optimize human health while organizations. The structure and function of current maintaining humane, safe, and economically viable systems are important for assessing current practices. swine and poultry production. Rhetoric, opinions and There is particular focus on the Canadian perspective anecdotes are not acceptable foundations for wide- including surveillance, responsibility for AMU and AMR reaching policy, regulation, and legislation, but current regulation, current regulatory practices and issues, and knowledge gaps create an environment where such identified strengths and weaknesses within this system. subjective information can have major impact. This document identifies important concepts and practices While objective data regarding the links between AMU that should be considered for setting priorities, and AMR are variable and information on effective developing and implementing policy, regulation and interventions is sporadic and sometimes contradictory, legislation, and educating all relevant stakeholders. both the livestock industry and regulatory bodies have

2 national collaborating centre for infectious diseases Methods

This project reviews the literature on the ecology and a high rate of duplicates (approximately 40%), of antimicrobial resistance (AMR), AMR in zoonotic thus further databases were only used to address and commensal bacteria with the potential to cause specific inclusion criteria. The citations identified by foodborne disease, antimicrobial use (AMU) in pigs the searches were evaluated using a priori relevance and chickens, and the surveillance of AMU and screening criteria that elaborated on the inclusion AMR in pigs and chickens. It evaluates the literature and exclusion criteria. All relevant publications were describing the relationships between AMU and AMR briefly summarized as to which inclusion criteria as well as the policies, strategies, and interventions to they addressed. control AMR in bacteria carried by chickens and pigs. Throughout this document, the term ‘antimicrobial’ is Because of the volume of publications identified, defined as, “any substance of natural, semi-synthetic, a supplementary search strategy was applied to or synthetic origin that kills or inhibits the growth of a ensure critical publications were prioritized. A series microorganism but causes little or no damage to the of searches was completed using only the Medline .” (4) and is used in the context of inhibiting or database to identify articles indexed by the following: killing bacteria. i) terms similar to foodborne, food, animal origin, antimicrobial resistance, or antibiotic resistance; Publications utilized in this project were obtained and terms similar to Escherichia coli, Enterococcus, either through publication databases subscribed to Salmonella, Campylobacter; MRSA or Clostridium by the University of Saskatchewan library or through difficile; and terms similar to swine, pig, pork, poultry, known resources (both written and personal) that broiler, or chicken; ii) terms related to antimicrobial the authors were aware of, or in contact with, as use in the broiler or swine industry, microbial ecology, a result of their expertise in this area. The authors or relationship between AMU and AMR and; iii) terms preferentially utilized peer-reviewed scientific designed to look at the potential association between literature. When publications were unavailable or AMR in chickens and pigs and AMR and health in insufficient, the alternatives of reports, websites humans. This search was limited to publications since and personal communications were employed. 1999 to emphasize the most current developments Relevant databases were identified and prioritized to in the field. Again, the search strings and number of ensure the literature search was comprehensive but citations identified were recorded. Duplicate articles not redundant. were removed and the results were saved in an electronic reference manager software (Refworks ©). The study inclusion and exclusion criteria were The resulting data files were exported into a custom defined (Table 1) and used to establisha priori designed database, using Microsoft Access, for search terms, search strings, and medical subject reviewers to describe and search the content of each heading (MeSH) terms (Appendix 1). Searches were paper for relevance to the project. restricted to English publications and the years 1990 to 2009. A professional librarian conducted each Two veterinary epidemiologists independently search, recorded the identified citations, and acquired reviewed citation titles and abstracts and excluded necessary full texts. Three databases were searched citations that did not meet the inclusion criteria. systematically using consistent search terms: CAB, The title and abstract of the remaining citations Embase, and Medline. Two databases were searched were used to describe the publication by a series systematically with terms tailored to the database of dichotomous variables that included the bacterial content: Agricola and Scopus. These searches species, livestock species, stage of production or returned a large number of citations (> 3,500) processing, AMU data, and type(s) of AMR data

www.nccid.ca 3 (, associations with human health, In addition to the journal articles, original research microbial ecology or relationship between AMU). was described in 21 conference proceedings, 19 The independent reviews were combined and reports, and 5 websites. Thus, 297 (55%) of the discrepancies discussed and agreed upon. The full citations refer to original research. The remaining publications were acquired and reviewed by the 242 citations (45%) were government reports author(s) of pertinent sections. (72, 33%), scientific reviews (136, 56%) and grey‑literature (27, 11%). The proportion of citations Following the conclusion of these searches, and that are original research is disproportionately low while describing and evaluating the literature, relative to the proportion of original research citations authors occasionally conducted ad hoc searches of identified in thea priori literature searches because publication databases, the Internet, or known grey many of the grey literature citations and government literature. These results of ad hoc searches were not reports were intentionally sought out to address the recorded. All authors reviewed the entire document. project objectives. An external review was graciously provided by veterinary epidemiologists specializing in swine, poultry, antimicrobial resistance, and surveillance techniques from the Public Health Agency of Canada.

As a result of this process this report cites 539 references. The majority of references (n = 360, 67%) are articles published in journals. Of these, 252 (47%) describe original research, 98 (18%) are reviews, and 10 (2%) describe government programs or research. These journal articles were published between 1977 and 2009; 13% were published prior to 2000, 65% were published between 2000 and 2007 and 22% were published in 2008 or 2009. The remaining 179 citations reference books (26, 5%), websites (44, 8%), conference proceedings (29, 5%) and reports or monographs on the internet (80, 15%).

4 national collaborating centre for infectious diseases Table 1. Comprehensive review criteria for literature inclusion and exclusion.

Category Inclusion Exclusion Exposure Route Foodborne Non-foodborne Exposure route Direct contact with animals Direct consumption Occupational exposure Exposure to raw meat Environmental Bacteria Zoonotic Pathogens Animal pathogens Salmonella Environmental bacteria Campylobacter jejuni Human pathogens infecting animals Campylobacter coli Animal commensals beyond list Clostridium difficile Yersinia enterocolitica Listeria monocytogenes MRSA Commensal Escherichia coli Enterococcus Pharmaceuticals Antimicrobials Antifungals Antimicrobials used in humans or veterinary medicine Antivirals Antimicrobial feed additives Hormones Ionophores Vaccines Sectors Swine Farm Boar studs Abattoir Wild boar operations Commodity boards Wild animals Broilers Broiler breeder Layers Hatchery Eggs Growers Turkeys Abattoir Minor species (duck, quail) Commodity boards Wild birds All other food or livestock sectors Governments Agriculture departments Governments below federal level Health departments International agencies Support Industries Veterinary associations Pharmaceutical industry Nutrition/feed companies

www.nccid.ca 5 Chapter 1: The Hazard of Antimicrobial Resistance in Foodborne Bacteria

Introduction is devoted to describing concerning pathogen/ resistance combinations. Some are well known, like People are increasingly affected by antimicrobial Campylobacter and Salmonella, while others are resistant bacteria; they can be exposed to bacteria either of secondary importance to Canadians, such through many environmental connections, one as Yersinia enterocolitica, or emerging food safety of which is the food they eat daily. Through food, concerns such as Clostridium difficile. The relevance people can be exposed to antimicrobial resistant of resistance in these foodborne resistant pathogens zoonotic pathogens and commensal bacteria. for Canadians is the focus of this chapter. Foodborne bacteria typically originate in the animal’s gastrointestinal tract and reach people through fecal contamination of meat at slaughter. The The Link Between AMR Bacteria in gastrointestinal tract provides an ecological reservoir Animals and Humans that supports a diverse bacterial population. Most Bacteria are ubiquitous in our environment and often bacteria in this population are beneficial or neutral to infect multiple animal species including humans. The the animal host and are not the target of antimicrobial probability that people will be infected or colonized drug use. However, antimicrobial exposures intended by bacteria from animals is affected by the route of to kill pathogens or improve growth also affect these exposure, frequency of exposure, the exposure dose, bacteria. Resultantly, the normal flora becomes an and the host-adaptation of the bacteria. Bacteria unintended casualty or develops/acquires resistance. carried by animals that can cause disease in humans When people consume enteric bacteria through are termed ‘zoonotic.’ The disease caused by these contaminated food, the bacteria are returned to a zoonotic bacteria can be exacerbated if the bacteria similar ecological niche and can either cause disease are resistant to antimicrobials (8–10). In addition, or share resistance elements with the diverse bacterial antimicrobial resistant bacteria can be a source flora resident in people (5–7). of resistance elements for bacteria harboured by people (11–13). Direct physical contact, shared Scope and Objectives environments, and exposure through vectors and The objective of this section is to provide sufficient are all routes for bacterial transmission knowledge of the hazards to public health, the between animal species. This review focuses on source of bacteria, and the resistance types of foodborne bacteria. greatest concern to facilitate the evaluation of The dominant link between most Canadians the programs, policies, and strategies to control and viable bacteria from animals is likely food AMR that have been created by regulators and consumption. Resistant bacteria undoubtedly the agriculture industry. This chapter is limited to spread into the environment through aerosol and describing antimicrobial resistance (AMR) in bacteria animal wastes (14–16). However, modern livestock that infect people through food. It is restricted to production has greatly reduced the frequency and discussing resistance as it pertains to chicken and extent of contact between humans and agricultural pigs/pork. This limitation in scope does not infer that animals. Only 2.2% of Canadians live in the farm these commodities pose a different risk to people population; the remaining 97.8% have limited direct than other meat commodities. After describing how contact with animals and their environment is largely people are exposed to resistant bacteria, the biology separate from the airspace and properly managed of AMR is explained. The main body of this chapter waste of livestock (17). People in direct contact with

6 national collaborating centre for infectious diseases animals face different hazards and have different risk people (27–30). Transmission can theoretically occur factors for acquiring AMR bacteria and, while further from commensal bacteria originating in livestock to study is required to clarify the extent that resistance pathogens in humans, or vice versa, from commensal spreads to people by these routes, these links are bacteria in humans to pathogenic bacteria in beyond the scope of this project. livestock. Although this contribution is indirect, it may pose a risk to humans that is equal to or even Antimicrobial resistance directly affects human greater than that posed by pathogenic bacteria. health when with pathogenic bacteria Commensal bacteria are ubiquitous in healthy leads to illness that requires antimicrobial therapy animals and can contaminate carcasses at slaughter. and the selected therapeutic is ineffective due to The high prevalence of these bacteria drastically resistance. This results in prolonged illness with increases the probability of exposure compared to potentially more severe symptoms. The worst case pathogenic bacteria. scenario is a bacterial infection that is refractory to all available treatments leading to death (9,10,18). Although treatment failure is the most obvious Introduction to AMR Ecology effect from AMR, other health hazards exist due to Resistance Development AMR in bacteria. Numerous studies show the risk of hospitalization and the severity of disease are greater Antimicrobials either kill (bacteriocidal) or inhibit in people acquiring a resistant bacterial infection (bacteriostatic) bacteria. Not all antimicrobials compared to those with a similar but susceptible are effective against all bacteria: bacteria that are strain (19–23). This increases the cost of treatment intrinsically resistant lack the structural or functional and the burden on the health care sector, and places cellular mechanisms that are required for the people at risk for exposure to other nosocomial antimicrobial to act (4,31). Intrinsic resistance is a infections (10,24). The increased disease severity genus or species-specific property of bacteria (32). may partially be related to ineffective treatment early While it is necessary to understand that some bacteria in the disease and subsequent disease progression. are inherently resistant to certain antimicrobials, this is But increased hospitalization and disease severity is not the focus of this review; therefore, the remainder reported even after accounting for ineffective therapy. of this report will pertain to acquired AMR. Acquired This could be due to co-selection of virulence traits, resistance occurs due to a change in the bacterial up-regulation of virulence traits, or improved fitness genome. The two major ways that susceptible of resistant strains (25,26). Antimicrobial resistance bacteria acquire AMR are through mutation or also increases the incidence of foodborne disease as horizontal acquisition of foreign genetic material people taking antimicrobials for any reason have an (31,33). increased likelihood of being colonized by resistant bacteria because the therapeutic drug alters the Mutation body’s normal flora and concurrently selects for Mutation is a spontaneous change in the genome resistant bacteria (9,18). resulting in a susceptible bacterium becoming resistant, usually during replication (33). Two types of resistant foodborne bacteria contribute Chromosomal mutations often result in structural to health burdens. Resistant pathogenic bacteria changes to the bacterial cell wall which subsequently directly contribute to all four effects described above: confers resistance (4,31). Mutation may lead to treatment failure, increased hospitalization rates, dramatic resistance development or to slower more increased disease severity, and increased disease gradual resistance development depending on the incidence. Resistant commensal bacteria indirectly antimicrobial agent affected (4,31). Mutants may contribute to the problem by harbouring and be disadvantaged compared to the parent and, spreading resistance genes to bacteria pathogenic to therefore, less able to survive in the population in the

www.nccid.ca 7 absence of the selective pressure of an antimicrobial. genetic elements such as plasmids, transposons, Alternatively, mutants may be as or more viable or integrons/gene cassettes (35–37). These than the original strain and may persist in the elements can possess multiple AMR genes and population with or without selective pressure from may be responsible for the rapid dissemination the antimicrobial (34). The emergence of resistance of resistance genes among different bacteria from mutational events happens at high frequencies (28,38,39). Linked clusters of resistance genes on for drugs such as streptomycin, nalidixic acid, and a single mobile element can aggregate in such a rifampin and has not been reported for others such way that antimicrobials of a different class or even as vancomycin and polymixin B (4). non-antimicrobial substances like heavy metals or disinfectants can select for AMR bacteria (40,41). Horizontal Transfer of Resistance Exchange of resistance genes between pathogens The horizontal transfer of resistance genes from donor and non-pathogens or between gram-positive and to recipient bacteria is a second method through gram-negative bacteria has been documented (40). which bacteria can acquire resistance. Transformation, transduction, and conjugation are the three primary The Spread of Resistance: means for the horizontal transfer of resistance Mobile Genetic Elements genes (35). Of the three mechanisms for horizontal transfer of resistance genes: transformation, transduction, Transformation is the uptake of naked bacterial DNA and conjugation, conjugation is undoubtedly the from the environment by acceptor bacteria (4,35). most important to understand. The acquisition of It is an important method of gene transfer in vitro genetic elements such as plasmids, transposons, but less important in vivo (32). Transformation or integrons/gene cassettes is a critical part of generally occurs between closely related genera and horizontal transfer of AMR because these elements may result in gene recombination producing new connect and re-assort resistance mechanism forms of resistance genes. This method of resistance thus enabling the spread and establishment of transfer is particularly important in bacteria species resistance elements in bacteria populations. These such as Streptococcus and Neisseria that have a high elements vary considerably from each other in frequency of natural transformation (4). regard to their carriage of resistance, their replication, Transduction is the transfer of resistant genes via a and transmission. bacterial virus or phage (4,35). This is thought to Plasmids are extra-chromosomal circular DNA that can be a relatively unimportant method of resistance replicate independently of chromosomal DNA. When transfer because bacteriophages are very specific to resistance is transferred via plasmids, a copy of the the bacterial host and can carry a limited amount plasmid is retained by the donor cell. Most plasmids of DNA; but occasionally, resistance plasmids can carry the gene required for conjugation, but not all do. be accidentally packed into phage heads during In these cases, plasmids can be mobilized by using phage assembly and subsequently be able to infect the conjugal apparatus of other self-transmissible new cells by injecting plasmid DNA into a recipient plasmids within the cell (4,32). Plasmids can harbour cell (4,32). Neither transformation nor transduction resistance genes for between one to ten different requires a viable donor cell or a link between donor antimicrobials (multiple AMR) (4). Multi-resistant and recipient (31). plasmids are often the result of interplasmidic Conjugation is the transfer of resistance genes recombination, integration of transposons, or insertion from a donor to a recipient bacteria through of gene cassettes (32). All resistance genes on a a temporary protein channel (4,35,36). Gene multi-resistant plasmid are transferred when the transfer in conjugation allows the spread of mobile plasmid is transferred, whether there is selective

8 national collaborating centre for infectious diseases pressure for all of the resistance genes on the to relevant antimicrobials (43,44). Integron carriage plasmid or for just one of the resistance genes (32). of resistance gene cassettes by host bacterium can Plasmids can act as vectors for transposons and be dependent on the environment; host bacteria can integrons/gene cassettes (36). potentially lose integron-borne resistance genes in the absence of antimicrobial selective pressure (45). Transposons (jumping genes) are short sequences of DNA that can move from plasmid to plasmid, or from Resistance Selection: Direct Selection, plasmid to chromosome, and vice versa. Transposons Cross-resistance and Co-selection do not possess replication systems and must be incorporated into chromosomal DNA or plasmids As mentioned earlier, the development of AMR (32). Unlike plasmids, no copy of the transposon is a complex process and the speed with which remains within the original cell as the transposon it develops depends on the bacteria involved, moves between the donor and recipient. All the selective pressure, and the availability and transposons can move and integrate into foreign DNA transferability of resistance genes (32). Recent by non-homologous recombination, which permits studies have shown that the majority of multi- the same transposon to be found in the genome or resistant phenotypes are obtained by the acquisition plasmids of highly unrelated organisms (4). of external genes that may provide resistance to an entire class of antimicrobials (46). Antimicrobial Integrons are a mobile element often found on use can select for antimicrobial resistant bacteria in plasmids and are distinct from transposons. They are three ways: direct selection, cross-resistance, and a site-specific recombination system consisting of an co‑selection. integrase enzyme, a gene-capture site, and a captured gene cassette(s). Each gene cassette encodes a Direct selection is the most simplistic form of selective single resistance gene and a specific recombination pressure and occurs when a drug selects for bacteria site (4,41,42). An integron’s site-specific integrases resistant to it. For example, tetracycline is used and recognizes gene cassettes and catalyzes their tetracycline resistant bacteria survive. Cross-resistance insertion at a specific site. Repetition of this sequence occurs when the expression of one antimicrobial results in integrons linking together multiple resistance resistance gene infers resistance to several related gene cassettes (4). drugs that have similar targets or mechanisms of action. The blaCMY-2 gene provides an example of Gene expression of an integron is dependent on cross-resistance. This gene confers resistance to many various factors including promoter strength, gene potentiated ß-lactams (ampicillin and amoxicillin- copy number, the relative distance of the gene clavulanic acid) and cephalosporins (ceftiofur, cassette from the promoter, and the presence of cefoxitin, and ceftriaxone). Therefore, exposure to additional internal promoters. Expression is usually ceftiofur will both select for bacteria carrying this gene mediated via a common promoter situated upstream and indirectly increase the frequency of resistance (5’-end) of the gene cassettes, rather than through to ampicillin. Cross-resistance is also common in the individual promoter copies. Higher levels of gene macrolide and fluoroquinolone classes (4). expression can be achieved if a second promoter is included adjacent to the first, or if the gene in Co-selection is the phenomenon of antimicrobial question is included as multiple copies. The relative use selecting for resistance to completely unrelated distance between a gene cassette and the promoter drugs. Bacteria with multiple resistance genes can plays a significant role regarding expression; proximal survive exposure to any drug affected by these genes. genes tend to be expressed more effectively than Therefore, the use of any of these drugs perpetuates distal genes. As a result, distal genes may have very resistance to all of the unrelated antimicrobials for little effect on the susceptibility of the host bacterium which bacterium possesses resistance genes. (4).

www.nccid.ca 9 Co-selection has important implications for policies of human infections are caused by C. jejuni while designed to eliminate existing resistance and C. coli accounts for 5 to 10% (50,53). Although contributes to the complex relationship between less significant thanC. jejuni, C. coli can rank among antimicrobial use and resistance development (use the top four causes of enteric infection in people of drug A can select for resistance to drug A; but and should not be discounted as a food-safety because of co-selection, it may also be selecting for concern (54). resistance to drugs B, C, and D). Campylobacter primarily cause sporadic disease Phenotype versus Genotype and to date, an effective typing system has not been developed. Together, these factors make source Information on both the resistance genotype and attribution difficult (55). Poultry is considered a phenotype are valuable in evaluating resistance. leading source for foodborne infections while the role Genotype data illustrate the diversity and distribution of pork is less clear (56–59). Chickens generally carry of resistance, which improves our understanding of C. jejuni as part of their commensal flora and pigs transmission and selection. Phenotype data provide typically harbour C. coli (56,60–63). Although both an indication of the susceptibility of the organism and pigs and chickens commonly carry Campylobacter at is of clinical relevance. Phenotype and genotype AMR slaughter, retail meat sampling consistently identifies results may not correlate completely. Bacteria can much higher Campylobacter recovery rates from have a resistant phenotype and susceptible genotype poultry than red meats (64–66), presumably because if the active resistance genes were not considered in chicken intestines are more friable and prone to testing or are novel and not yet identified. Conversely, breaks that can cause carcass contamination. Case a susceptible phenotype and resistant genotype control studies routinely aggregate C. jejuni and C. coli can arise if genes are incompletely expressed, cases. This may cause risk factors unique to C. coli confer resistance below the phenotypic threshold, to be missed because C. coli accounts for a smaller or are non-functional (47,48). Because each proportion of cases and could partially explain why provides different information, considering both the pork is not consistently identified as a risk factor for phenotype and genotype provides a more complete Campylobacter infection (67). understanding of AMR. It is believed that resistant cases of human AMR in Foodborne Bacteria campylobacteriosis generally arise from acquiring a resistant strain, versus human therapeutic drug Zoonotic Bacteria use selecting for resistance (23,68). Initially, this seems counterintuitive given that resistance arises Campylobacter rapidly following therapy in people. However, AMU in Campylobacter is the leading reported cause of uncomplicated cases is contraindicated so exposure bacterial foodborne enteric infections in many in people should be limited. In contrast, antimicrobial developed nations. Most cases are mild, self-limiting consumption prior to an infection can increase the and do not require antimicrobial therapy, but severe risk of a resistant infection in people (69), which cases can be prolonged, progress to septicaemia or suggests that human AMU provides a competitive extra-intestinal infection, and require antimicrobial advantage to already resistant strains. Campylobacter therapy (49). In Canada, approximately 12,000 are ubiquitous in healthy pigs, so long durations of cases are reported annually with an estimated 23 to AMU can result in a prolonged and pervasive selective 29 unreported illnesses per reported case (50,51). pressure on the Campylobacter population to acquire Campylobacter can be contracted from both food resistance and establish resistant strains. In reality, and water but warm blooded animals are the only attributing resistance in Campylobacter to agricultural site of amplification (52). Eighty to ninety percent AMU is difficult as it requires data on AMR in isolates

10 national collaborating centre for infectious diseases prior to therapy and should account for AMU prior 1.6% of the C. jejuni and 3% of the C. coli were to infection. The resistance rates in Campylobacter resistant to macrolides (87). The rate of resistance in isolated from Canadians are available from regional human infections is highly variable world wide; rates research projects (70–72), but not from national as high as 51% in Singapore and 80% in Nigeria surveillance. The most recent results from American have been reported in Campylobacter isolates from surveillance found over half of the Campylobacter children (88). tested were resistant to one or more Clinical Laboratory Standards Institute (CLSI) antimicrobial Macrolide resistant Campylobacter are relatively rare classes and 13.6% were resistant to two or more in chickens (generally <1%) but are prevalent in subclasses (73). pigs (generally >50%) (66,79,89). This difference is partly due to the predominance of C. coli in Campylobacter’s most concerning resistance types pigs and C. jejuni in broilers; C. coli are genetically are macrolides and fluoroquinolones. Ciprofloxacin predisposed to macrolide resistance. This species is a frontline drug for undifferentiated gastroenteritis, characteristic is so strong that 40% of Campylobacter so fluoroquinolone resistance may cause treatment from antibiotic-free swine farms have been identified failure. High level fluoroquinolone resistance occurs as macrolide resistant. This could reflect intrinsic with a single-step chromosomal mutation in the gryA resistance, persistence of acquired resistance from (60,74). Resistance to fluoroquinolones inC. jejuni historical AMU, or transfer of resistance that arose from poultry and humans is very common in certain from AMU in other groups of pigs on the farm parts of the world, including Mediterranean Europe (90,91). Campylobacter from pigs also demonstrate and South East Asia (53,75–77). In comparison, more macrolide resistance due to extensive macrolide almost complete susceptibility to ciprofloxacin is use in swine (84). Comparing macrolide use reported in C. jejuni from Australia, Norway, and between pigs and chickens is hampered by different Sweden (78–81). In poultry, emerging resistance in drug-use metrics, but over half of Canadian swine C. jejuni correlates with the use of fluoroquinolones producers use macrolides in feed while less than 5% and this resistance does not appear to impose of chickens in America are exposed to macrolides a fitness cost, and may even be advantageous (66,85,92,93). (34,49,82). No fluoroquinolones are licensed for use in pigs or chickens in Canada although The food safety hazard posed by macrolide resistant injectable enrofloxacin could be used in an extra‑label Campylobacter could plausibly increase in the future. manner. The rates of ciprofloxacin resistance inC. Over 20 erm genes have been identified, which are jejuni from retail chicken ranged from 0 to 2.3% the genes responsible for many of the mutations in from different parts of the country in 2006 (66). the rRNA genes that cause cross-resistance between National surveillance for AMR in Campylobacter macrolides, lincosamide and spectinomycin. These from pigs is not conducted in Canada, but Canadian erm genes exist in gram-positive and gram-negative research projects have reported 2.4 and 10% bacteria and many are located on transmissible ciprofloxacin resistance inCampylobacter from pigs genetic elements. Acquisition of these genes, along on farms (83,84). with Campylobacter’s ability to pick up heterologous DNA through transformation, makes the likelihood Resistance to macrolides is also concerning in of macrolide resistance establishing in C. jejuni a Campylobacter because this antimicrobial class is concern (88). Because C. jejuni predominates in prescribed for severe cases of campylobacteriosis human disease, this could have a far greater human or immunocompromised cases. This has raised health impact than the current high rates of macrolide concern over widespread macrolide use in veterinary resistance found in C. coli. medicine (85,86). From American human cases,

www.nccid.ca 11 Salmonella sites, it will provide insight into the food sources of Salmonella for Canadians (96). Non-typhoid Salmonella are a leading cause of bacterial gastrointestinal disease worldwide. Most Not all Salmonella serovars cause disease in all cases are self-limiting, but severe cases can become hosts. For example, S. Cholerasuis and occasionally invasive and cause extra-intestinal infections. In S. Typhimurium can cause clinical disease in pigs, many developed nations, the incidence of reported and S. Gallinarium, S. Pullorum, and occasionally enteric infections from Salmonella is second only S. Enteriditis can cause disease in chickens to Campylobacter. Canadians report 6,000 cases of (100,101). Chickens and pigs can carry many other Salmonella annually, and for each reported case, an serovars that rarely cause overt disease in their animal estimated 13 to 37 cases go unreported (50,51). The host but regularly cause disease in people. The most global incidence of resistance in Salmonella infections common serovars causing human disease worldwide appears to be rising; and in Canada, over one-third are S. Enteriditis and S. Typhimurium (98,102). Along of human clinical isolates are resistant to at least one with these, S. Heidelberg is a predominant serovar antimicrobial and 11% are resistant to five or more in North America (66,103). Controlling zoonotic (66,94,95). Salmonella serovars in food animals is the impetus for on-farm Salmonella control programs, as opposed Ninety to ninety-five percent of non-typhoid to control of epizootic serovars. Salmonella infections are foodborne (96–99). Salmonella causes both disease outbreaks and The most direct threat posed by AMR in Salmonella sporadic infections. Disease outbreaks are more likely is treatment failure following use of an antimicrobial to be detected by surveillance as the likelihood of to which the infecting strain is resistant. Accordingly, medical involvement increases with the number of resistant infections are associated with higher case cases. However, outbreaks represent unusual events fatality ratios and increased hospitalization rates and and can substantially bias source attribution given durations (19,20,104,105). In addition to more the large proportion of infections that go unreported severe disease, AMR may cause a higher disease (96). Surveillance often implicates meat, most incidence. A Danish model found that relative to commonly chicken, less frequently pork, and eggs their prevalence, quinolone-resistant Salmonella as causes of Salmonella infections (97–99). Food caused more disease than would be expected than surveillance most commonly isolates Salmonella quinolone-susceptible Salmonella. Also relative to from fresh meat, again more commonly from poultry their prevalence, multidrug-resistant Salmonella were than pork, and less frequently in eggs, beef, fishery associated with more illness than would be expected products, vegetables and fruit, and milk (97). This compared to pan-susceptible Salmonella. This trend shows that the food safety risk from certain sources, was consistent across all serovars modelled. It was such as contaminated vegetables, can be overstated proposed that this trend could be due to enhanced by disease outbreaks. ability to survive food processing or increased susceptibility in people consuming antimicrobials The source of Salmonella infections can vary for other indications (98). Collectively, these depending on diet and geography, and over time, studies demonstrate that antimicrobial resistance the prevalence and serovar distribution of Salmonella in Salmonella creates a health burden additional to in food-animal populations can change. All of these baseline salmonellosis and that the increased burden factors affect human case attribution. Canadian is not limited to a particular serovar. attribution data are not currently available, but a surveillance program for enteric disease (C-Enternet) Public health officials recognize two resistance types has been established in Waterloo, Ontario. As this in Salmonella pose an undue threat to human program expands to its planned five or six sentinel health. These include resistance to fluoroquinolones,

12 national collaborating centre for infectious diseases the main treatment for invasive salmonellosis, and become extended spectrum ß-lactamases and resistance to newer generation cephalosporins, the the other was through the emergence of the indicated treatment for salmonellosis in pregnant plasmid‑mediated Ambler class C (AmpC) enzymes, women and children (86,106). Historically, predominantly mediated through CMY- genes. fluoroquinolone resistance was conferred by two Each enzyme hydrolyzes a slightly different set of stepwise chromosomal mutations, and therefore, cephalosporins (114). resistance only developed when bacteria were exposed to a fluoroquinolone and subsequently only In humans, resistance types tend to cluster transmitted vertically to progeny. Over the last few geographically, but extended spectrum ß-lactamases years, plasmid-mediated fluoroquinolone resistance and AmpC resistance both occur in Europe and North genes have been reported in Europe, Asia, and the America. In animals, extended spectrum ß-lactam United States (107–111). resistance genes predominate in Salmonella in Europe with the few reported cases of AmpC-type The emergence of horizontally transmissible resistance in European livestock linked to imported fluoroquinolone resistance genes raises two concerns. animals (111,114). In North American food animals, First, these can be transmitted between Salmonella Ambler class C enzymes predominate and are and E. coli in vitro, and presumably, in vivo (107). generally mediated by the blaCMY-2 gene. Across This exponentially increases the bacterial reservoir North America the major foodborne source of ESBL that can harbour these genes and eliminates species resistant Salmonella differs. In Mexico, multidrug- or geographical barriers to the dissemination of resistant S. Typhimurium carrying blaCMY-2 are resistance. So far reports of plasmid-mediated the primary cause of ESBL resistant Salmonella quinolone resistance genes in animals are rare, but infections. The blaCMY-2 gene has been identified it appears inevitable that these genes will become in children with diarrhea and a foodborne link was established in livestock and poultry (74,107). This made to pigs (19). In Canada and the United States, will further exacerbate control efforts regarding the most concerning serovar for ESBL resistance is fluoroquinolone resistance. The second concern S. Heidelberg and the main food-animal reservoir is that the emerging qnr genes that moderate appears to be poultry, as determined from retail fluoroquinolone resistance can be associated with meat surveillance in these countries (66,73,115). In mobile genetic elements with novel combinations addition to sampling retail meat, the Public Health of resistance genes including extended spectrum Agency of Canada tests isolates and reports AMR ß‑lactam resistance genes (ESBL) (107,112,113). This from clinical cases of Salmonella in people. In late drastically increases the likelihood of treatment failure 2003, 30% of the human S. Heidelberg infections as these are the two drug classes most commonly from Quebec were resistant to ESBL. By 2004, this used to treat Salmonella. Potentially of equal concern had risen to almost 50% of the cases. Concurrent is that use of drugs outside the fluoroquinolone class with this rise, a sharp increase was observed in can now supply the selective pressure necessary to ceftiofur resistant S. Heidelberg in retail chicken establish and disseminate fluoroquinolone resistance. sampled from eastern Canada (see Chapter 2 Figure 2) (116,117). The role of poultry as a main Public health authorities are also concerned about source of S. Heidelberg in Canadians has been ESBL resistance in Salmonella. In the 1980s, supported by a case control study (118). resistance was predominantly due to broad spectrum ß-lactamases that hydrolyzed penicillins and older The epidemiology of AMR in Salmonella can relate generation cephalosporins (TEM-, SHV-, CTX-M-). to serovar. This was clearly recognized with the In the 1990s, resistance to newer cephalosporins global dissemination of the infamous S. Typhimurium emerged through two routes: one was via minor DT 104 clone carrying resistance to ampicillin, mutations of broad-spectrum ß-lactamases to chloramphenicol, streptomycin, sulfamethoxazole,

www.nccid.ca 13 and tetracycline (ACSSuT) (119,120). The ACSSuT role as an indicator of meat contamination, E. coli resistance was carried on a chromosomal island, thus from healthy animals have also been adopted as an was vertically disseminated within this serovar (120). indicator of AMR for gram-negative bacteria. E. coli Yet, the predominance of blaCMY-2 in S. Heidelberg are used to understand resistance in bacteria with demonstrates that certain Salmonella serovars can complex ecologies such as Salmonella. Although have an affinity for particular plasmid-mediated a relationship does exist between serotype and resistances or plasmids. Salmonella serovars and resistance types in E. coli, this relationship is largely clones can shift independent of AMU, but shifts ignored in E. coli isolated from healthy animals (aka can also be influenced by AMU (121). This makes generic E. coli). This is valid because, as opposed it difficult to understand how AMU is affecting to pathogen overgrowth, a diverse population of Salmonella epidemiology in general and resistance E. coli can concurrently exist in the gut which differs in particular. The relationship between serovar and from the clonal populations seen with pathogen AMR also makes it difficult to generalize about the overgrowth. The ubiquity, simple isolation, and prevalence or patterns of resistance in Salmonella. diversity of E. coli makes it as a good model for This challenge is addressed by limiting discussions understanding AMR in Salmonella because the genes to a specific serovar or, as will be discussed, operating in Salmonella also operate in E. coli and circumvented by using generic E. coli as an indicator can be transmitted between these bacterial species for Salmonella in particular and gram-negative (27,107). bacteria in general. Although E. coli is a useful model for AMR in Salmonella, differences certainly exist. The same Commensal Bacteria resistance phenotypes, and often genes, operate in E. coli these bacteria, but their behavior and transmission can differ. For example, the genes encoding the Salmonella and Campylobacter clearly demonstrate ACSSuT phenotype in S. Typhimurium are located on that bacteria can be transferred from animals to the bacterial chromosome yet when this resistance people through food. These zoonotic pathogens phenotype is identified inE. coli, the genes are cause disease in people, and if the strain is resistant, typically located on plasmids. Furthermore, the value it can increase the disease burden. However, these of E. coli for understanding AMR in Salmonella does bacteria represent a small fraction of the total not extend to predicting resistance in Salmonella possible spread of resistance elements to people based on resistance in E. coli on a farm or regional through food. The normal bacterial flora responds level (124). This limitation is at least partly due to to antimicrobial exposures by establishing resistant differences in the location and transmission of these populations. Fecal contamination of meat at slaughter genes in each bacterium as well as an inability to is one mechanism that can result in human exposure account for the relationship between resistance and to these bacteria, and once consumed, genetic Salmonella serovar. exchange with pathogenic or commensal bacteria in the human gastrointestinal tract can occur. While Escherichia coli are used to study the selective transmission rates remain unknown, the sheer pressure on the gram-negative bacterial population to volume of these bacteria makes many experts believe develop and retain resistance. The intestinal normal that the global threat from AMR may be more greatly flora is not the target of antimicrobial treatments, impacted by this commensal reservoir than emerging but nevertheless these bacteria are exposed and resistance in pathogens (12,122). become resistant—much like civilian casualties in war. The degree of resistance in E. coli mirrors this Fecal contamination of food is generally monitored selective pressure on gut bacteria (48,125,126). through recovery of (123). Expanding on the E. coli Thus the greatest utility of studying AMR in E. coli is

14 national collaborating centre for infectious diseases improved understanding of the health risks posed by gram‑negative commensal bacteria, studying the antimicrobial use. prevalence and determinants of AMR in E. coli can improve our understanding of AMR epidemiology in a As an indicator organism, the main resistance diverse set of human pathogens. outcomes of concern in E. coli are those that are a concern in Salmonella. Resistance Of course, E. coli is not only important as an indicator to fluoroquinolones and newer generation organism. E. coli can be pathogenic. Verotoxigenic cephalosporins are monitored closely. In contrast E. coli (VTEC) cause symptoms from diarrhea to to the relatively rare reports of plasmid-mediated haemorrhagic colitis and haemorrhagic uraemic fluoroquinolone resistance inSalmonella from the syndrome. This virulence type is frequently expressed agri-food sector, several reports of plasmid-mediated by the O:157 serotype but is not exclusive to that resistance in E. coli exist (108,127–129). Detecting strain (25,132). VTEC infections are predominantly emerging resistance is much simpler in E. coli than foodborne and associated with beef. Human Salmonella simply because large, representative illness from VTEC is largely independent of AMR. isolate collections can be assembled quickly and Antimicrobials are contraindicated in VTEC cases economically. E. coli is also useful for understanding because this can induce release of the verotoxins, the reasons for changing AMR in Salmonella. so treatment failure is a relatively minor concern Through retail chicken surveillance in 2004, the (133). The attributable fraction (i.e. infection in Canadian Integrated Program for Antimicrobial people taking antimicrobials that select for a resistant Resistance Surveillance (CIPARS) noted the rise in foodborne pathogen) also seems small as studies ceftiofur resistance in S. Heidelberg was mirrored that have compared AMR rates in VTEC and non- in E. coli (66). This provided supporting evidence VTEC from healthy animals have found lower rates that resistance was changing due to antimicrobial of resistance in the VTEC isolates (although higher drug pressures rather than the emergence and rates of resistance may be reported in isolates from dissemination of a resistant Salmonella clone. sick animals, these have likely been exposed to therapeutic AMU and are not representative of the Resistant gram-negative bacteria, including E. coli, background rate of bacteria that may contaminate are part of the resistance reservoir that can spread food) (134,135). In pigs, the concern that resistance elements from animals to people. E. coli antimicrobial use could select for virulent E. coli was from mice, chickens, and humans can exchange raised because statistical relationships were identified resistance genes (130). Integrons from multidrug- between resistance and virulence genes (26,136). resistant E. coli from animals and human cases The virulent isolates were obtained from sick pigs of urinary tract infection (UTI) had identical gene and thus raised an animal health question. However, cassettes and configurations, and these gene similar relationships between resistance and virulence cassettes were also identical to isolates sequenced genes in E. coli from healthy animals would be a food from around the world. The authors raised the issue safety issue because this would suggest antimicrobial of food animals acting as an integron reservoir, with use could increase the prevalence of virulent isolates global and cross-species transmission, for AMR and increase foodborne disease risks. One study transmission to human commensal and pathogenic of E. coli from healthy pigs destined for the food bacteria (30). Resistance gene transmission is not chain found no relationship between virulence and limited to pathogenic E. coli. Resistance elements resistance genes (48). Based on the main source can be transmitted to numerous pathogens, both of VTEC being beef and relatively minor human within and beyond the Enterobacteriacia family health concerns from AMR, pathogenic E. coli are not (27,28). Multi-resistant gram-negative infections addressed further in this project. are increasingly important in human medicine (131). If these are acquiring resistance genes from

www.nccid.ca 15 Foodborne E. coli may also be related to human thinking outside of the box. Our understanding of illness from extra-intestinal pathogenic E. coli (ExPEC). the epidemiology of foodborne E. coli infections Clusters of urinary tract infections (UTI) caused by is still emerging, and to our knowledge, no studies clones of uropathogenic E. coli raised the hypothesis have evaluated the severity of disease or cost of that people shared a common infection source, treatment of resistant versus susceptible infections which could be food (137,138). This hypothesis has where resistance is directly or indirectly attributed been investigated using traditional and molecular to gene transfer from commensal bacteria. From epidemiology: a case-control study compared this summary, it is obvious that much more remains the dietary habits of women with susceptible and unknown than is presently known. resistant infections and found consumption of pork and poultry were each risk factors for specific Enterococcus resistance phenotypes (139). Recent work on avian Antimicrobial resistance in enterococci is monitored pathogenic E. coli and uropathogenic E. coli from for three purposes. First, enterococci are an human cases found that within a particular strain, indicator organism and serve as the gram-positive O1:K1:H7, the genomes of avian and human isolates indicator organism. Like E. coli, enterococci are were highly similar. This was interpreted as supporting commensal bacteria that are ubiquitous in healthy the hypothesis that some avian pathogenic E. coli animals including humans. They can survive in the may act as a foodborne source of uropathogenic environment after release from their animal host E. coli for people. Johnson et al. concluded that and can reflect the antimicrobial selective pressures there is “no convincing genetic evidence for host experienced in their host (141–143). Secondly, or syndrome-specific pathotypes ofE. coli within enterococci have ready ability to accept and transfer ExPEC,” and called for further investigation to AMR genes. Congruent transposons have been determine the extent of the relationships between found in pigs, pork and people indicating resistance animal and human pathogens (140). These results elements are mobile across animal species (144). have expanded the realm of food safety concerns Enterococci can also transfer resistance genes to from foodborne bacteria and will undoubtedly be other bacteria. In particular, concerns exist over the investigated in future research. potential spread of vancomycin resistance from enterococci into multidrug-resistant When the potential for pathogenic E. coli to cause Staphylococcus extra-intestinal disease is taken into consideration aureus. Such transfer has occurred experimentally and a limited number of human infections have been along with the potential for E. coli from animals to share AMR genes with a variety human commensal reported (145–148). and pathogenic bacteria, it becomes clear that The third and arguably most important reason to the effects of foodborne resistant bacteria are study AMR in enterococci is because they are among wide‑reaching (27,30,130). Together, epidemiology the most important opportunistic pathogens in and molecular genetics are elucidating ecological people and resistance can affect treatment protocols. links between people and animals, and bacteria Approximately 60% of enterococcal infections are and their transmissible genes, which until now have nosocomial (149). Infections are predominantly been discussed but largely unsupported. Hence, caused by E. faecalis (80 to 90%) and to a what was plausible is increasingly appearing possible, lesser extent E. faecium (5 to 10%), although although the prevalence of these connections remain the proportion attributed to E. faecium is rising unknown. These recent developments demonstrate (149–151). Enterococci are intrinsically resistant that risks from resistant bacteria are unpredictable to cephalosporins, fluoroquinolones, clindamycin, and that complete understanding of the relationship trimethoprim-sulfonamides, and low doses of between AMR in animals and people will require aminoglycosides, and E. faecium also have variable

16 national collaborating centre for infectious diseases susceptibility to ß-lactams (106,150). Acquired were resistant to vancomycin (73,115). In contrast, resistance to a variety of drugs further limits available VRE were prevalent in pigs and chickens in Europe treatment options for these infections (150). prior to the ban on avoparcin, a related glycopeptide that was licensed for use in animal feeds (141–143, Resistance to vancomycin and quinupristin/ 155,156). The ban of avoparcin seemed to have dalfopristin (QD) are among the greatest current an impact on VRE; for example, Denmark banned concerns in treating enterococci infections. These avoparcin in 1995 and reported 43% glycopeptide concerns are related because streptogramins have resistance in E. faecium from broilers and 21% in been used to address vancomycin resistance. This E. faecium from pigs in 1996. By 2000, resistance discussion largely applies to E. faecium because had declined to 6% of the E. faecium in both broilers acquired resistance is less common in E. faecalis and pigs (157). (150). Numerous genes confer vancomycin resistance: vanA concurrently infers teicoplanin In Europe, but not North America, there is a large resistance and is one of the most prevalent and community reservoir of VRE (149). Foodborne concerning genes (150). Resistance to vancomycin exposure to VRE or transmission of resistance genes emerged in the late 1980s and over the course of from livestock to humans through food may have a decade rose to account for 25% of all enterococci played a role in the establishment of VRE in the blood-borne infections in the United States European community because experiments have (24,152,153). Because nosocomial infections with shown transient colonization with animal-derived E. faecium are less prevalent than E. faecalis, and E. faecium (158) and human acquisition of the vanA vancomycin resistance occurs more commonly in gene from contaminated food (29). But the role of E. faecium, by 2002 this translated to rates of 75% food as a source of human disease remains uncertain resistance in E. faecium in some American hospitals because illness is rarely caused by the same strains of (152). The extent of this problem varies between E. faecium as are found in livestock, and community- countries. Over half of the European countries acquired infections are rare (149,156,159,160). involved in nosocomial surveillance reported <1% While ecological connections between VRE in pigs, vancomycin resistance in their already extremely low chickens, community carriers, and ill people appear to rates of invasive E. faecium infections. Yet Greece, exist, much remains to be learned about their relative Ireland, and Portugal reported more than 25% of importance. For example, E. faecium collected over a the invasive E. faecium infections were vancomycin decade from hospitals, community infections, swine resistant (151). This puts substantial burden on and poultry were compared, and some clonal groups the health care system as these infections cause contained isolates originating from more than one more severe disease than vancomycin-susceptible source, but overall the groups largely held isolates infections (24). from one source (161). No risk assessments were identified describing the probability of avoparcin use In enterococci from pigs and chickens, vancomycin in livestock and poultry resulting in treatment failure resistance is mediated by the vanA gene cluster from vancomycin-resistant E. faecium. This is now an carried on the horizontally transmissible Tn1546 academic curiosity, as avoparcin has been removed transposon, which is the same transposon and from the world market (162). gene found in many human vancomycin-resistant enterococci (VRE) (149,154). Vancomycin resistance In the late 1990s, a streptogramin antimicrobial, is rare in enterococci from North American food quinupristin/dalfopristin (QD) (Synercid®), was animals. Canadian surveillance of retail chicken and released to treat multidrug-resistant gram-positive pigs on farms has found no VRE (66). In the United infections. Primary indications included vancomycin- States, none of over 6,700 enterococci obtained from resistant E. faecium (E. faecalis are innately resistant) chicken carcass rinsates between 2003 and 2006 and MRSA infections (162). Shortly after the release

www.nccid.ca 17 of QD, streptogramin-resistance was recognized in Bacteria of Secondary Interest E. faecium. Once again, agricultural antimicrobial use was questioned because virginiamycin (a Yersinia enterocolitica streptogramin) is used as a feed-grade antimicrobial. Yersinia enterocolitica is often ranked as the third Virginiamycin use can select for the vat(D) or vat(E) or fourth most common foodborne bacterial genes which infer resistance to dalfopristin. These pathogen following Campylobacter, Salmonella and genes do not cause full resistance to virginiamycin occasionally E. coli O:157. Yersinia enterocolitica or QD because they affect streptogramin A but causes acute gastritis, diarrhea, abdominal pain, and not B. However, streptogramin B targets the same fever, and children have increased rates of infection ribosomal subunit as macrolides and lincosamides (64,97). The reported incidence rates are similar and can be affected by resistance mechanisms in this in Ontario (2.3 cases per 100,000 person years) antimicrobial class (163). Thus QD resistance may (national estimates not available) and Europe (2.8 be selected for by virginiamycin and macrolide use in cases per 100,000 person years) (96,97). Finland, livestock. Prior to the release of QD, virginiamycin was Germany, Lithuania, and Sweden have reported not related to any antimicrobials used in humans. higher rates (6 to 15 cases per 100,000 person European countries banned virginiamycin on the years) while the incidence is lower in the United precaution that it could select for resistance to QD. States (0.4 cases per 100,000 person years) (166). The United States and Australia both conducted The dominant pathogenic strains differ slightly in quantitative risk assessments evaluating the human Europe and North America (97,167,168). health risk from virginiamycin use in food-producing Yersinia enterocolitica primarily causes sporadic animals (162,164). In 2004, Australia revoked the infections so source attribution is difficult (97). label for virginiamycin use for growth promotion Outbreak investigations and meat contamination and/or improved feed conversion and required rates suggest that pigs are the main livestock reservoir modifications to the label for prophylactic and for foodborne infections (64,169,170). Yersinia therapeutic claims. In contrast, neither the United enterocolitica is a commensal in pigs. Other species States nor Canada changed the label indications also carry Y. enterocolitica, but these belong to the or drug availability. In North America, virginiamycin non-pathogenic 1A biogroup. On a ranked basis, continues to be extensively used in poultry and the reported prevalence in slaughter hogs tends minimally used in pigs (66,92,93,165). Canadian to correlate with reported human incidence rates: surveillance (2006) of E. faecium from retail chicken Germany, 67%; Canada, 42%; United States, 13% found 50% to 75% resistance depending on the (167,170,171). However, caution should be used province of origin. In near-to-market pigs (2006), when comparing these prevalence estimates because 24% of the 37 E. faecium isolates tested were the sampling and laboratory methods differed resistant to quinupristin/dalfopristin (66). In people, between studies. Data were not available from many linezolid is now often used preferentially over QD to countries, making this comparison incomplete. treat multidrug-resistant enterococci because of fewer side effects. Canadian surveillance found no linezolid Extra-intestinal Yersinia infections can require resistant enterococci in retail chicken or near-to- antimicrobial therapy. Broad-spectrum cephalosporins market pigs in 2006 (66). with or without aminoglycosides are generally effective as are fluoroquinolones, trimethoprim- sulfonamide combinations and doxycycline. Antimicrobial susceptibility to ß-lactams is serogroup specific with some strains possessing chromosomally

18 national collaborating centre for infectious diseases mediated ß-lactamase genes (168). The resistance processing systems means that L. monocytogenes conferred by these genes to penicillins and typically causes outbreaks rather than sporadic cephalosporins is not entirely predictable but does infections (173). Many domestic animals can harbour not extend to newer generation cephalosporins such L. monocytogenes, which can lead to retail meat as ceftriaxone or cefoxitin. contamination. Retail meat testing in Ontario found 7% of pork chops and 28% of skin-on chicken German and Canadian surveys of Yersinia from pigs breast were contaminated (96). Ready-to-eat foods found that resistance to drugs other than ß-lactams are at increased risk of causing disease because this or erythromycin is rare (167,170). Isolates from bacterium can multiply at refrigeration temperatures. meat in Greece largely corroborated this, with no Canada, the United States (US) and the European reported resistance to 3rd and 4th generation Union (EU) prohibit the sale of products containing cephalosporins or fluoroquinolones. Low rates of ≥ 100 cfu/g of L. monocytogenes (106,174,175). resistance were noted to streptomycin, tetracycline, and co‑trimoxazole, but isolates were obtained Effective treatment includes early diagnosis and from a variety of sources and were not exclusively antimicrobial therapy. Choice antimicrobials are Y. enterocolitica. Statistical associations were identified typically a penicillin or ampicillin in combination between certain resistance phenotypes and virulence with an aminoglycoside. Cases allergic to ß-lactams genes (172). Similar findings inE. coli have been may be treated with a trimethoprim/sulfonamide interpreted as an increased potential for antimicrobial combination, tetracycline, or chloramphenicol use to select for virulent strains (26,48,136). (176). Vancomycin and erythromycin are indicated Therefore, interventions that minimize AMU in pigs for use in pregnant women (173). To date, could potentially decrease the morbidity attributed AMR has not been a major concern with clinical to Yersinia. L. monocytogenes infections. Studies that have examined L. monocytogenes from meat have found Listeria monocytogenes almost complete susceptibility to penicillin, ampicillin The Listeria genus consists of six species, but only and aminoglycosides. Resistance to tetracycline and L. monocytogenes is an important foodborne fluoroquinolones is more variable and high rates of pathogen. Mild infections typically present with resistance to sulfonamides, but not trimethoprim- flu-like symptoms. More severe cases can cause sulfonamide combinations, have been reported septicemia, meningitis, and miscarriage or stillbirth. (176–181). Listeria monocytogenes are intrinsically The case fatality rate from L. monocytogenes resistant to cephalosporins (106). can be as high as 30% (173). The incidence of While resistance to clinically relevant drugs is L. monocytogenes infections is low relative to other currently very low, it is still of some concern given foodborne bacterial pathogens. Europe and the that not all patients can be treated with penicillins. United States report 0.3 cases per 100,000 people Case reports of resistant infectious strains exist, (97,166). People with impaired T-cell immunity are at and isolates with transposons and plasmids increased risk for infection. This group includes young carrying antimicrobial resistant genes have been children, elderly people, pregnant women, and the identified (176,182,183). From these, it has been immunocompromised (97,173). determined that L. monocytogenes can acquire Main reservoirs of L. monocytogenes include soil, resistance elements from other gram-positive forage, and water. Environmental contamination bacteria, particularly Enterococcus and Streptococcus and cross-contamination of food in meat processing while transiting the gastrointestinal tract (176,183). facilities are key factors in foodborne transmission Enterococci carrying multi-resistance to ß-lactams and of L. monocytogenes. The structure of modern food aminoglycosides exist which makes the potential for

www.nccid.ca 19 resistant Listeria monocytogenes that are refractory to focused on methicillin resistance. This resistance, treatment a concern. Monitoring of this pathogen will conferred by the mecA gene, provides resistance be important to ensure human therapy is predictable to all ß-lactam antimicrobials including methicillin, and to allow interventions should resistance become penicillins, cephalosporins, and carbapenems. a problem, which would be devastating in such a This gene is carried within the staphylococcal virulent pathogen. cassette chromosome mec (SCCmec) and, once acquired, is stable within the bacterial chromosome. Emerging Issues Staphylococcus aureus carrying the mecA gene are referred to as methicillin-resistant Staphylococcus The following section presents two bacteria that aureus (MRSA) (184,185). do not directly fit this project’s inclusion criteria of foodborne resistant bacteria. Despite this, The 1960s saw the emergence of MRSA as a it is imperative to discuss methicillin-resistant nosocomial pathogen (hospital-acquired MRSA or Staphylococcus aureus (MRSA) and Clostridium HA-MRSA). Over the last two decades, MRSA has also difficile because concerns are escalating over the become established in people outside of hospital public health risk from these bacteria in food animals. settings (community-acquired MRSA or CA-MRSA) For both bacteria, concerns are being fuelled by a (106). Studies have estimated that 1.5% to 3% of lack of information on the hazard. These bacteria the North American population are colonized with remind us of the importance of ‘thinking outside- MRSA (186–188). Infection with MRSA is associated the-box.’ Neither pathogen has been traditionally with increased mortality and higher treatment costs considered zoonotic. Due to unique concerns and compared to infection with methicillin-susceptible limited information on these novel problems, the S. aureus (MSSA) (24). Serious infections lead organization of the following sections differs from the to 19,000 American deaths annually with 84% preceding bacteria. attributed to HA-MRSA and 14% to CA-MRSA (189).

Methicillin-Resistant Staphylococcus There are major lineages within S. aureus that can Aureus show host specificity for humans or animal species; this specificity extends to MRSA. Within a geographical Staphylococcus aureus are gram-positive bacteria area certain lineages or clones dominate, and these that can colonize the skin or nose and mouth of can differ between hospitals, the community, and people and animals. Staphylococcus aureus is a agricultural settings. The clones associated with common commensal in humans and can be found each setting tend to have somewhat predictable in the nasal passages of approximately 30% of phenotypic characteristics and virulence traits (184). healthy individuals. Colonization rates are variable This discussion focuses on a specific clone relevant in other species. Colonized individuals are a source to food safety, hereafter referred to as livestock- of infection to others and are at greater risk for associated MRSA (LA-MRSA). Other descriptions infection themselves. ßeta-lactamase-mediated of MRSA are limited to the minimum necessary penicillin resistance is very common in S. aureus, so to provide context for understanding the role of ß-lactamase-resistant penicillins are a main treatment LA‑MRSA as a potential foodborne pathogen. for community-onset S. aureus infections. There may be various other therapeutic options as a range Staphylococcus aureus is an animal pathogen. of antimicrobials are potentially effective against Because of the clonal lineage, diseases in humans S. aureus. However, S. aureus has a tendency to and animals were historically considered unrelated. develop or acquire antimicrobial resistance and This view has changed over the last decade with multidrug-resistant staphylococci are a leading the recognition that dogs, cats, and horses can be health concern in human medicine. Much of this is colonized with and clinically affected by pathogenic

20 national collaborating centre for infectious diseases MRSA strains that are indistinguishable from human tissue infection, pneumonia, and septicemia in strains (190–192). Epidemiological evidence people. Across the EU, LA-MRSA accounts for 0.7% suggests that infection in these species resulted from of typed MRSA isolates, but the rate varies between a spill-over from humans; such transmission has been countries; higher rates are reported in countries that dubbed a ‘humanosis.’ These animal infections create have low overall rates of MRSA and high exposure to a human health risk because people exposed to pig farming (184). carrier animals can be infected by MRSA. The zoonotic potential of LA-MRSA has raised Concern over MRSA in animals expanded when concerns that LA-MRSA could be a food safety a clonal strain, sequence type 398 (ST398), was hazard. Food has served as a in a hospital identified in pigs (193). Further study identified a high outbreak of MRSA but food handlers, rather than prevalence of this clone in pigs, as well as some other animals, were considered the primary source (201). livestock types, and an association between human Theoretically, colonized animals could contaminate infection or colonization with this strain and contact carcasses and meat during slaughter and create with food animals. Subsequently, MRSA associated a source of exposure for people. MRSA has been with this clone has been referred to as LA-MRSA. In detected in numerous foods of animal origin contrast to the situation in companion animals, the including chicken and pork (202–207). The majority LA-MRSA clone is distinct from previously common of these studies found only human-related strains, human strains. Since its identification, LA-MRSA has which is suggestive of meat contamination from been found in pigs in Austria, Belgium, Canada, food handlers. The exceptions were a single pork Denmark, France, Germany, the Netherlands and sample by van Loo et al. and the study by de Boer Singapore. As summarized by the European Food et al. which found more than 90% of the MRSA Safety Authority (EFSA), the reported prevalence from chicken, pork and a variety of other meats were of LA-MRSA in pigs is high in these countries LA-MRSA (204,205). Although a large proportion of (184): Europe, 10% to 39%; United States, 70%; tested meat samples were positive for LA-MRSA, the Canada, 25% (194–199). Caution should be degree of contamination was below 10 cfu/g. Similar exercised in comparing these prevalence estimates results have been found for retail meat in Canada, because sampling and laboratory methods were with MRSA being identified in retail pork, and beef, not standardized. To date most investigations have albeit at very low concentrations (208). Currently, focused on swine, thus pigs are often considered a beyond the 1995 report suggesting, but not proving, primary reservoir of LA-MRSA. However, veal calves, that food prepared by a colonized hospital worker dairy cows, and broiler chickens can be positive and was the source of an MRSA outbreak in a hospital may be important in the epidemiology of this clone (201), there are no reports of food as a source of (184). In general, LA-MRSA does not cause clinical human MRSA infection. disease in colonized agricultural animals. LA-MRSA is frequently multidrug-resistant, but For people working directly with food animals, the pattern differ from CA-MRSA and HA-MRSA. LA‑MRSA is an occupational hazard. Direct contact Resistance to tetracyclines is observed in almost with colonized livestock can result in human 100% of LA-MRSA isolates, and resistance to colonization or infection with LA-MRSA (193). trimethoprim, but not trimethoprim in combination Colonization risk increases with exposure: the highest with a sulfonamide, is common. Fluoroquinolone rates occur in people that work directly with pigs resistance has been reported from 0% to 35% (29%), followed by people entering barns but not (197,209). Based on this multi-resistance pattern, working with pigs (12%), then people not working therapeutic treatment options are limited to valuable with pigs but living on positive farms (2%) (200). classes of drugs including the oxazolidinones and LA‑MRSA has been associated with skin and soft pleuromutilins. Resistance to these drugs can be

www.nccid.ca 21 conferred by the cfr gene. This gene affects the colonized individuals, people with CDI, the binding sites of 23S RNA and infers resistance environment, pets, food, and water (218–227). This to antimicrobials with this target site including section of the report focuses on the potential role oxazolidinone, pleuromutilins, phenicols, lincosamide, of food in CA-CDI. The main factor that has led to and streptogramin A. Two S. aureus isolates, one of suspicion of foodborne transmission is the similarity which was a LA-MRSA clone carrying the cfr gene, of food animal and human CA-CDI strains. Currently were identified in pigs in Germany. Although not an in people, PCR ribotype 027 is the most important indication of its prevalence, this report heightens clone while ribotype 078 is increasingly attracting concerns over limited treatment options should attention. Both of these clones are found in HA and LA-MRSA become more established in agricultural CA-CDI cases (228–235). Although still preliminary, animals and subsequently people (210). toxinotype V strains, predominantly ribotype 078, may be overrepresented among CA-CDI isolates The European Food Safety Authority has determined (228,229,236). that current evidence indicates the food safety risk from LA-MRSA is small and is much lower than the The following section exclusively discusses C. difficile risk from exposure to colonized animals or humans in pigs and chickens. Readers should be aware that (184). Staphylococcus are killed by heat and will parallel knowledge is emerging in other meat-animal be eliminated with cooking or pasteurization. This commodities. Ribotype 078 has been reported in pigs limits the food exposure risk to unpasteurized dairy from different countries (237,238). In an American products and meat that is consumed raw or minimally study, 83% of C. difficile isolates from pigs were cooked. The risk of exposure from handling meat ribotype 078 (237). Although far less investigated, also appears low as reports of colonization in meat C. difficile has been identified in chickens (239,240). handlers are infrequent. Reports of C. difficile in food animals led to concerns about the potential for retail meat contamination. An Clostridium difficile American study reported C. difficile contamination in Clostridium difficile is the most commonly identified 47% (21/45) of examined pork products (225). In cause of antimicrobial-associated diarrhea and that study, 67% of positive pork products harboured health care-associated (HA) diarrhea in most areas ribotype 078 while the remainder harboured ribotype worldwide and is responsible for virtually all cases of 027. A study of retail pork using samples collected pseudomembranous colitis (211,212). Clostridium from four Canadian provinces only identified difficile infection (CDI, previously called C. difficile- C. difficile in 1.4% (4/296) of ground pork and associated diarrhea or CDAD) is also emerging as 3.1% (3/97) pork chops (241). The most common an important cause of community-associated (CA) strain was ribotype 027 and ribotype 078 was not diarrhea with dramatic increases in the incidence found. A second Canadian study of ground pork rate reported over the last decade (213,214). Severe found C. difficile in 12% (14/115) of samples but CDI is now being reported in populations previously most samples had low numbers of C. difficile and considered to be at low risk with unique features were only positive with enrichment culture (242). that had not described including close contact Where numbers could be determined, samples transmission, high recurrence rate, young patient age, typically contained only 20–240 spores per gram. bloody diarrhea, and lack of antimicrobial exposure While the infectious dose of C. difficile is not (215–217). known, it is assumed that low levels are of lesser concern than high levels. Further, one considers that The source of infection of people in the community C. difficile can be found in treated water, vegetables, is unclear. Various sources are possible, including and the household environment, so it is clear that

22 national collaborating centre for infectious diseases simple exposure to low levels of C. difficile is not bacterial populations and their animal hosts, between the sole factor in the pathophysiology of disease urban, rural and agricultural environments, and (219,243,244). between bacterial hosts. Transmission and evolution can involve re-assortment of linked resistance genes, Determining the relevance of C. difficile in food which consequently alters the selective pressures animals to CA-CDI will require much more from co-selection. This has forced scientists and policy investigation. Unanswered questions include the makers to seek solutions that extend beyond limiting reasons for different ribotypes in American and the use of one antimicrobial in an attempt to mitigate Canadian livestock studies and the correlation a single resistance outcome. between C. difficile types found in retail meat and those found in healthy food animals at slaughter. This chapter also presented many foodborne links More work is also needed on the prevalence of between AMR bacteria in pigs and chickens and contaminated meat and the degree of contamination. humans. However, what is possible is not necessarily If meat is commonly contaminated with C. difficile probable. Although experimental and observational at levels sufficient to cause disease, it could be studies have described many transmission routes, the important in the epidemiology and control of CA-CDI. probability of each occurring is often conditional on numerous sequential events. We felt it was important The concerns over antimicrobials and C. difficile to describe these routes, but do not mean to leave differ from the other bacteria described in this report the impression that every bacteria and resistance type because therapeutic failure in humans is a minor described are in a crisis situation. concern. Instead, the concern with antimicrobial use is disruption of the normal intestinal flora and In conclusion, this chapter has presented numerous subsequent overgrowth of C. difficile. The recent recent developments. These include the emergence recognition of a possible foodborne link and of plasmid-mediated fluoroquinolone resistance, different concerns for AMR in C. difficile explain the description of the cfr gene, and an emerging why studies to date have focused on elucidating connection to animals for the traditionally human- potential transmission routes between food animals based diseases of MRSA and C. difficile. These and people. Future studies may study AMR in discoveries are shaping our approach to food safety C. difficile from food animals, with an application and zoonotic disease. They remind us of the need to of understanding on-farm practices that affect the be constantly alert and that what we think we know epidemiology in livestock populations. today will likely be questioned tomorrow.

Conclusion This chapter has summarized the main foodborne hazards that humans face from antimicrobial resistant bacteria in food animals. It has focused on specific resistance types in individual bacterial species. This ‘drug-bug’ orientation is necessary to understand the issues that influenced many policies and regulations to control AMR. However, many scientists are evolving from a ‘drug-bug’ perspective to an ecological approach. This has been largely driven by the recognition that barriers to resistance exist only in our minds. Resistance elements move between

www.nccid.ca 23 Chapter 2: Antimicrobial Use

Introduction The development and spread of AMR is a complex process involving interactions among antimicrobials, Antimicrobial resistance (AMR) is an important issue microorganisms, and the surrounding environment facing both human and veterinary medicine. The (249). There are multiple sources that may contribute increasing number of antimicrobial resistant pathogens to the creation and dissemination of AMR (Figure 1). in human medicine has raised both public and scientific interest. For human pathogens, most of the While there is evidence indicating each pathway AMR development is considered attributable to the exists, our knowledge of the importance of each selection pressure from antimicrobial use (AMU) in remains incomplete (Figure 1) (12). There are many people (245). However, the volume of antimicrobials routes for AMR to spread within a local environment, used in food animal production has led to concerns including but not limited to, spread between humans, in the public, regulatory, and scientific arenas that livestock, companion animals, wildlife, fish, water and AMU in food animals is contributing to the AMR soil, and vegetables (12), but the global aspect of problem by creating a reservoir of resistant bacteria AMR is also important to consider especially in the (134,246,247). For human health, the transfer of context of international travel, animal movement, and such resistance to zoonotic enteropathogens is of food trade. primary interest, but the development of antimicrobial resistance in animal pathogens, the associated The complex ecology of AMR development and subsequent loss of therapeutic options for veterinary dissemination can create considerable challenges medicine, and the potential need to use antimicrobials in determining how much each potential source of greater importance in human medicine is also an impacts AMR development in humans. As the important concern. issue of AMR is further explored and investigated, it becomes increasingly difficult to evaluate often While AMR is an issue in veterinary medicine in conflicting results or statements with regard to the Canada, its overall clinical impact is much less role of each of these potential sources. This point than in human medicine. However, the continued can be argued as being a fundamental question that development of AMR in human medicine and needs to be addressed or a question of academic the occurrence of AMR as a veterinary problem interest. It is the division between these two schools in other parts of the world indicate that AMR may of thought that have lead countries to implementing become more of a concern in Canada with regard to either evidence‑based AMR policy or a precautionary continued therapeutic efficacy in veterinary medicine principle based-approach. (248). The use of antimicrobials in animal agriculture is important for maintaining and improving animal Scope and Objectives health and welfare through disease prevention and In order to understand the potential impact that treatment, and arguably for increasing carcass quality, swine and poultry production may have on AMR as well as for enhancing the economic efficiency development, the literature was examined and of growth and production. If the livestock industry an overview was compiled. The objectives of this loses efficacious antimicrobials because of resistance chapter are to: highlight the reasons for AMU in development, or experiences limited access because swine and broiler chickens, review the classes of of tighter regulations, the consequences and costs antimicrobials used and the utility of continued to the industry are difficult to quantify but have the availability of efficacious antimicrobials in Canadian potential to be substantial.

24 national collaborating centre for infectious diseases Figure 1. Epidemiology of the potential major pathways for antimicrobial resistance to transfer. After Linton (250), modified by R. Irwin, reproduced with permission.

swine and broiler chicken production, describe current General Considerations, known risk factors for AMR development in bacteria isolated from pigs and chickens and the potential Terminology, and Reasons for relationship with AMR bacteria isolated from humans, Antimicrobial Use and discuss the information gaps that still remain in Different AMU regimens can select for various our understanding of the effect of AMU in livestock resistance genes (251), and therefore, AMU on public health. This chapter provides examples patterns are expected to have some impact on the rather than exhaustively listing all antimicrobial use distribution of AMR phenotypes (252–254). Among practices, risk factors or proposed links between the ramifications associated with resistance gene AMU in livestock and AMR development in humans. selection are the degree of resistance conferred and It is intended to provide a broad background for all the carriage of linked resistance determinants (251). readers regardless of their familiarity with agriculture Sometimes only minimal antimicrobial exposure and the issue of AMU in livestock and its impact on is necessary to select for continued persistence of human health. resistance genes within enteric microflora (251).

www.nccid.ca 25 Persistence of AMR in bacteria is generally related type of AMU. It was these classes of drugs that were to the persistence of antimicrobial use/exposure, revoked in the 1999 and 2006 European Union drug but AMR may also persist in the absence of known bans (259,260). antimicrobial selective pressure. An example of this is provided by a study of the University of Kentucky The terminology surrounding AMU for growth swine farm. This farm ceased all antimicrobial use and promotion is less precise in North America. then followed the animals housed on the farm over Regulations have always permitted feed-antimicrobial a period of 126 months. Resistance to tetracycline labels to claim improved growth, disease prevention declined by less than 50% over this time, leading and therapy. In the 1970s and 1980s, the United the authors to conclude that long-term withdrawal States government investigated the potential of antimicrobials failed to markedly reduce AMR and implications to human health from feeding that long-term feeding of antimicrobials could lead to tetracyclines and penicillins to pigs and chickens AMR that may not readily be reversed by withdrawal (261,262). The evidence for potential human harm of antimicrobials (255). From this and other studies was deemed insufficient to justify action. As a result, (256,257) it seems that some resistant bacteria can neither Canada nor the United States changed the become stabilized in the intestinal tracts of animals veterinary drug legislation to separate production and become the dominant intestinal flora potentially and health indications and both countries have passing from one generation to the next (258). These allowed continued access to these products without findings therefore indicate the need to consider the a veterinary prescription (263,264). So in North long-term effects of AMU in any environment. America, there are no drug use characteristics that reliably distinguish between AGP and other types of Antimicrobial Growth Promoter in-feed AMU. Describing in-feed AMU by the reported Terminology reason for inclusion is the only valid mechanism to proportion in-feed AMU into AGP versus other effects. Popular debate over AMU in agriculture often refers to drug use for growth promotion. While many An outdated method of categorizing AMU as AGP is deem ‘growth-promotional AMU’ inappropriate to consider all feed-grade antimicrobials included in and potentially even unethical, what does this term diets at less than 200ppm for more than fourteen mean? The phrase ‘antimicrobial growth promotion/ days to be AGP (261,265). Effectively, this means promoter (AGP)’ was a descriptive term coined that in-feed AMU prevents sub-clinical disease. early in the history of agricultural AMU to describe Throughout this document, the acronym AGP the overt effects of including drugs in the feed of will exclusively refer to the regulated feed‑grade apparently healthy animals. It became ingrained in antimicrobial additives within Europe prior to their AMU terminology in the 1970s when the European prohibition. Outside of the European situation, Union separated agricultural AMU legislation into all other in-feed AMU is either referred to by two classes (See Chapter 3). One class contained the reported purpose of use (including growth non-prescription feed additives that producers could promotion) or, if that is not available, simply as access without veterinary involvement and all other in‑feed or feed-grade AMU. AMU (i.e. prophylactic, metaphylactic and therapeutic use of feed-grade, water-soluble, and injectable Reason for Antimicrobial Use antimicrobials) required a veterinary prescription in Livestock (259). In Europe, these uses were mutually exclusive Intensive livestock operations, such as swine meaning that an antimicrobial could not be licensed or poultry operations, are typically confinement in both categories. Thus European references to AGP agricultural systems. These are defined as systems AMU pertain to a very specific and distinguishable

26 national collaborating centre for infectious diseases where “the movement of animals is confined and the mass medication of a group of animals to prevent they are raised in high density, usually with stimulated the spread of disease when only a few individuals feeding, and weight gain optimized so as to decrease have been identified as infected. Prophylaxis is a time to mature weight.” (122). As demand for meat preventative treatment of an animal or group of grows, so does the confined livestock production animals at a time when it may be more susceptible because it allows for economies of scale. Traditionally, to infection (267). Antimicrobials are given at critical raising large numbers of animals in a close proximity points in production to help prevent the development often required the use of the tools of prophylactic, of disease. Prophylactic treatment may involve the metaphylactic, and growth promotional AMU in order entire group of animals or may be targeted toward to prevent morbidity and mortality, to ensure animal specific high risk individuals depending on the welfare, and for economic benefit. animal species, the production system, and the disease condition. It is not the need for AMU in livestock that is at question, but the extent to which antimicrobial use is Growth promotion is another reason for AMU necessary that is up for debate. Clearly animals can in livestock and it generally involves the use of be raised without routine use of antimicrobials under antimicrobials licensed for this purpose. Normally, some circumstances, but presumably there is always antimicrobials labelled for growth promotion are a need to access them if an animal or a group of included at a dose lower than those approved animals requires treatment. How far the industry can for therapeutic purposes and are fed for a longer go and needs to go in regularizing farming without duration than antimicrobials used for prevention antimicrobials is the question. The potential for and control (263). Long-term mass exposure to increased mortality, days to market, feed costs, and antimicrobials can increase the selection pressure for overall increase in the cost of production may need AMR development and persistence (268–271). to be passed on to the consumer resulting in higher food costs and precluding some individuals from Until recently in North America, the focus has been accessing animal-based protein sources. Therefore, a on minimizing the use of drugs of critical/very high balance between ensuring animal health and welfare, importance in human medicine for all purposes human health, and producing a reasonably priced including therapy and prophylaxis because these safe and wholesome product needs to be achieved. uses could increase selective pressure and the pool of bacteria resistant to these important antimicrobials In swine, the majority of antimicrobial use is for (272,273). Lately, in the United States there has treatment or prophylaxis of respiratory and enteric been increasing lobby to eliminate the use of disease, while in poultry, antimicrobials are primarily other antimicrobials, particularly AMU for improved used for intestinal infections, namely colibacillosis productivity rather than health purposes (274). and necrotic enteritis (265,266). The method of This more closely mirrors Europe’s premise that administration and the volume of antimicrobial used the human health risk from AGP does not justify its will vary depending on the animal species, stage continued use. In Europe, AGP AMU was of particular of production, and risk of disease. There are three concern because it was not strictly necessary for primary reasons for AMU in food-producing animals: health, and as it was responsible for the majority of treatment of sick animals, prevention and control of antimicrobial exposure by mass, it was presumed disease, and improved productivity. that this use caused most of the selection pressure leading to the indirect effect on the bacterial biomass Prevention and control can be further divided and the role of reservoirs in AMR transmission (275). into metaphylactic or prophylactic applications. Metaphylaxis is a disease control measure involving

www.nccid.ca 27 Antimicrobial Use Estimates generate useful national estimates, these data need to contain sufficient detail. Differences in record in Livestock Production keeping methodologies and priorities result a lack Many countries are attempting to gain a better of standardization and therefore summarizing understanding of the volumes of antimicrobials used information that is collected in multiple formats on in livestock production, but the problem is that these individual farms is extremely challenging. Capture of estimates can be misleading if the context is not use information can be expensive for the researcher understood. The main issue is that AMU data are and burdensome for the producer to accommodate difficult to collect and report. National, regional, or especially during times of additional demands with even farm level data are scarce. On a national level limited resources. Under-reporting is potentially a in numerous European countries, since antimicrobials problem since producers are busy with day-to-day are by prescription only, a central pharmacy database operations on the farm and, therefore, record keeping can provide information on the volume of AMU in may be relatively low on the priority list. Subsequently animals (35,79,89). Other countries like Canada treatment records may be forgotten or incomplete. and the United States are still working on the best Dunlop et al. (277) reported a 35% under-reporting methodology for collecting these data since they do rate for AMU recorded by swine producers as not have any legislation compelling pharmaceutical compared to inventory and disappearance data companies to provide this information nor do they collected by the research team. Reasons for under- have centralized pharmaceutical databases. reporting include misunderstandings between researchers and producers and lack of time during At the national level, AMU is often reported in periods of increased work load such as in disease kilograms or tonnes of active ingredient sold but outbreak situations (278). Current Canadian use can also be reported by divided daily doses producers may be less prone to under-reporting as (DDD) (276), animal daily doses (ADD) (276), or as Dunlop et al’s. study was conducted before on-farm animal‑units per treatment days (277). While each of food safety programs made AMU record keeping the above methods tries to capture the true exposure mandatory (See Chapter 4). Current producers have of an animal to a drug, they all are limited and much adjusted to maintaining AMU records but the accuracy debate still surrounds the best approach to reporting of these records has not been assessed. AMU information. Jensen et al. (276) provides a good overview and highlights the major potential methods Although there are several challenges associated for reporting drug use and the associated limitations. with AMU data collection in livestock, several In the case of reporting kilograms or tonnes of active countries are attempting to capture some AMU ingredient, while these data provide the volume of information. The next several paragraphs provide drug used, they do not allow for assessment of how some estimates of AMU in animals from various the drug was used and how this use may affect countries. While reviewing these numbers, it is AMR. Data on the species drugs are delivered to, important to keep in mind the limitations of reporting the number of animals exposed, the dose received, tonnes of antimicrobials used so as to not over or and the method of delivery are generally unavailable. misinterpret what these numbers are really telling us. Therefore, end-user data are often important to collect Also, comparing one country to another is difficult in order to gain a better appreciation of how and why because information on the denominator is lacking, antimicrobials are being used in livestock production. i.e. the number of animals, or the type of animal and/or the dose given. Without this information, it While end user data can provide valuable information, may appear like one country is using considerably it also has some serious limitations. Complete more antimicrobials in their livestock than another. and accurate farm/hatchery-level AMU records By not knowing how many animals were exposed are often difficult to obtain. In order to be able to and at what dose, etc., one cannot really compare

28 national collaborating centre for infectious diseases one country or region to another, since this may antimicrobial, followed by ionophores and macrolides equate to comparing apples to oranges. The main (66). These estimates were provided by the goal of presenting these data are to familiarize the Canadian Animal Health Institute (CAHI), which is the reader with how these data are often presented and trade association representing the companies that how they might be difficult to interpret and compare manufacture and distribute drugs for administration between regions and within species. to companion, sporting, and food animals in Canada (66). These data were aggregated to the class level Estimates of antimicrobial use in Europe in 1997 and represent the distribution of these antimicrobials were 10,494 metric tonnes (MT) of active ingredients in 2006; they therefore do not represent what was (35). Human use accounted for 52%, animal actually used during this timeframe (66). treatments for 33%, and growth promotion for 15% (35). In-feed use accounted for the majority In order to gain a better understanding of AMU and of the animal use with 90% of the antimicrobials to supplement this information, in 2006 CIPARS administered this way (35). The breakdown of the also began a pilot project to collect AMR and AMU total antimicrobial volume per species was as follows: information from Canadian swine herds. A preliminary pigs 60%, poultry and rabbits 20%, ruminants 18%, report was released that includes the first animal and fish and pets at 1%. For therapy, prevention, agriculture AMU data collected by this national and control, the antimicrobial classes used were program (66). From these first few years of farm tetracyclines (66%), macrolides (12%), penicillin surveillance, AMU data collection challenges and (9%), and others (12%) (35). limitations have been identified and data collection instruments have been refined to enable the team In the United States in 1989, the Institute of Medicine to gather the most useful AMU data available. While estimated that 50 million pounds of antimicrobials swine was the first commodity group that CIPARS were produced in the States annually and 50% of this began collecting data from, CIPARS has also been was used in animals (279). The Union of Concerned participating in large-scale research projects looking Scientists re-evaluated this and suggested that there at AMR and AMU in feedlot cattle, dairy cattle, and are 35 million pounds of antimicrobials used annually sheep production, and is currently in discussions in the United States with 87% of that being used with the poultry industry with regard to developing in animals (280). Non-therapeutic was the primary a farm surveillance program in this industry. Canada reason for use (280). In 1999, the Federal Drug is now facing challenges with how best to report Administration (FDA) and Center for Disease Control their farm‑based antimicrobial use data while and Prevention (CDC) began gathering AMU data acknowledging data limitations. from the Animal Health Institute. From these data, therapeutic and preventative use made up 83% In order to substantially contribute to our of the total (281). The drug classes used included understanding of AMU in animal production and aminoglycosides, fluoroquinolones, ionophores, its impact on AMR in people and/or animals, it is penicillins, sulfonamides, and tetracyclines. Current necessary to evaluate how antimicrobial use data are estimates of the volumes of antimicrobials used in collected and reported so that it can be optimally the United States are unavailable because at this time utilized. While this may intuitively be easy to do, the US does not routinely report AMU in livestock. the reality is it is a challenge that still needs to be overcome. Even human antimicrobial use does In the most recently available Canadian Integrated not seem to be accurately estimated and reported Program for Antimicrobial Resistance Surveillance (279,280), which leads one to surmise that there is (CIPARS) annual report, approximately 1.8 million kgs additional work that needs to be done to not only (~4 million lbs) of active antimicrobial ingredients understanding use in animals, but also in obtaining were distributed for animal use in Canada (66). more consistent AMU estimates in human medicine. Tetracyclines were the most commonly used

www.nccid.ca 29 Table 2. Antimicrobials licensed for use in pigs and chickens in Canada (2009).

Pigs Chickens Class Antimicrobial Feed Water Injection Feed Water Injectable Beta-lactam Ampicillin – – Pr – – – Ceftiofur – – Pr – – Pr Penicillin G OTC OTC OTC OTC OTC OTC Amoxicillin – Pr – – Pr – Sulfonamide Sulfonamide OTC OTC – – OTC – Trimethoprimsulfonamide – – Pr – – – Tetracycline Hydrochloride – OTC – – OTC – Chlortetracycline OTC – – OTC – – Oxytetracycline OTC OTC OTC OTC OTC – Macrolide Erythromycin – – OTC OTC OTC – Lincomycin OTC OTC OTC OTC OTC – Tiamulin OTC OTC Pr – – – Tilmicosin OTC – – – – – Tylosin OTC OTC OTC – OTC – Tulathromycin – – Pr – – – Aminoglycoside Apramycin – OTC – – – – Gentamicin – – Pr – – Pr Neomycin – OTC – – OTC – Spectinomycin OTC OTC – – OTC – Streptomycin – OTC OTC – OTC – Ionophores Salinomycin OTC – – – – – Streptogramins Virginiamycin OTC – – OTC – – Bacitracin OTC – – OTC – – Flavomycin Bambermycin – – – OTC – – Phenicols Florfenicol – – Pr – – –

OCT: available without a veterinary prescription; Pr: available with a veterinary prescription; –: no licensed products.

30 national collaborating centre for infectious diseases Antimicrobial Use: Routes, need be exposed. The limitations of parenteral AMU are feasibility in treating large groups of animals and Antimicrobials and Reasons animal stress associated with handling and restraint. for Use As pigs approach market weight, fewer herds use any injectable drugs and those continuing to use injectable A background on the swine and poultry industries and antimicrobials report lower exposure rates (277). This common production practices is available in Chapter 4 is because of animal handling and disease factors. and may assist those readers unfamiliar with these Market weight pigs are harder to handle and inject industries in considering the following information. As than small pigs. This increases the risk of injury to well, to further assist the reader, antimicrobials licensed the staff or the pig and the risk of needle breakage. for use in pigs and chickens in Canada are summarized Some provinces allow pigs with a broken needle to by the labelled administration route(s) in Table 2. be slaughtered if permanently marked while others Antimicrobial Use in Swine Production require all pigs with a broken needle to be euthanized. The increased likelihood of a broken needle and Swine producers around the world use antimicrobials greater economic loss from euthanizing older pigs both to treat and prevent disease, and depending on account for some of the decline in injectable AMU the country that they are being raised in swine, in near-to-market pigs. As well, there are decreasing can also be exposed to antimicrobials to improve infectious disease pressures as pigs age. However, feed efficiency and daily gain. Antimicrobials can be when health problems occur in near-to-market pigs, administered to pigs through feed, water, and injection. producers may choose to inject individual animals to Sows and suckling piglets are more often treated with avoid having to hold groups of pigs until antimicrobial injectable antimicrobials while nursery and grow-finish withdrawal times (period of time between the last pigs more often are administered antimicrobials as administration of the drug and the collection of edible groups through feed or water (93,277). tissue or products from a treated animal that ensures the contents of the residues in food comply with the Overall, AMU is a common practice in Canadian maximum residue limit for that drug) are observed. swine production. Data from CIPARS indicated that Additionally, producers may choose drugs with low or 75% of the participating herds were exposed to at no withdrawal period; in particular, drugs like ceftiofur, least one antimicrobial through feed, and 82% of the a third-generation cephalosporin, are used close to herds incorporated antimicrobials into either the feed market because of the zero day withdrawal. or water (66). Assuming that reporting feed or water AMU means that all pigs in the batch were exposed, In Chapter 1, the reasons for concern over resistance the majority of samples tested for antimicrobial development to new-generation cephalosporins and susceptibility within the CIPARS Farm program were fluoroquinolones were described. The use of these collected from pigs that had been exposed to an critically important drugs is discouraged by the World antimicrobial in the 20 weeks preceding sampling Health Organization (WHO) and Veterinary Drug (66). These estimates relate only to grow-finish hogs Directorate (VDD) (for further information on this but they do provide some estimates of conventional classification please refer to Chapter 3). Just under hog production antimicrobial use in this phase one-third of CIPARS sentinel herds used ceftiofur (66) of production. in grow-finish hogs. To date, no Canadian study has reported quinolone exposure (66,92,93,282,283). Injectable AMU is most important for treating clinically Fluoroquinolones are not licensed for use in pigs ill animals. The advantages of parenteral AMU are that or chickens in Canada, but injectable enrofloxacin the exposure to the appropriate dose can be ensured, (Baytril® 100, Bayer) is licensed in Canada for use treatment can be customized to each animal’s in cattle (263) and extra-label use (see Chapter 3 for condition, and only animals that require treatment definition) in swine is legal (284–286).

www.nccid.ca 31 In Canada, common injectable antimicrobials used including weaning or transportation. The antimicrobials include penicillin, trimethoprim-sulphadoxine, and can be mixed in precise amounts and are stable, oxytetracycline (92,93,93). Seventy-six percent of which makes it easier to achieve the desired CIPARS sentinel swine herds reported injectable concentration in feed than in water. Feed‑grade antimicrobial use in grow-finish pigs and the most medications are more cost effective than either water- commonly reported injectable antimicrobial used was soluble or injectable drugs. Feed-grade medications penicillin (66). are the only medication route used to improve growth.

Antimicrobials can also be administered through water. In Canada, most conventional swine producers use Water soluble antimicrobials can be administered to feed-grade antimicrobials and in many herds the groups of animals without stress and are more practical exposure to antimicrobials is extensive. A survey of for the treatment of infectious disease outbreaks than Alberta producers found 57% added feed medication parenteral medications. Unlike injectable antimicrobials, to weaner, grower, and finisher rations more than exposure is not ensured because sick animals may 95% of the time (93). Of the remaining 43%, feed stop drinking or may not drink sufficient water to medication was more commonly administered to achieve targeted blood antimicrobial levels. In this weaner and grower than finisher pigs (93). More regard, water antimicrobials are often an intermediate extensive use of feed-grade antimicrobial use in between injectable and feed-grade antimicrobials younger pigs has been reported by many studies and because animals typically cease eating before they quit is due to increased disease pressures and stressors in drinking. Water-soluble antimicrobials allow producers young pigs (92,93,282,283,287,288). to rapidly respond to changing disease situations in groups of animals because treatment can be initiated Tetracyclines, sulfonamides, and penicillin are and ceased virtually instantaneously with minimal commonly used in nursery pigs (93,287). Grow-finish labor. In contrast, medicated diets must be ordered pigs are most commonly exposed to macrolides for or made in advance and then administered until the disease prevention or growth promotion followed medicated feed is consumed. Despite these perceived by tetracyclines, which are predominantly used to advantages, fewer swine producers use water soluble prevent disease or treat respiratory disease (66). antimicrobials than feed-grade drugs. This is likely In-feed medication use is relatively static over time because administration requires supervision in the barn within herds. Dunlop et al. found few producers and physical infrastructure to deliver the medication. changed medication practices over eighteen months Water AMU is most common in nursery pigs (92,93). and Rajic et al. reported most producers used When investigated, much shorter exposure times are antimicrobials in diets more than 95% of the time in reported for antimicrobials administered through water the previous twelve months (93,282). Un‑medicated than feed (66,92,277,287). rations were more common during the latter part of the grower-finisher period (66). The use of In grow-finish pigs, 36% of Canadian producers un-medicated rations later in the feeding period reported use of water medication over a one year most likely relates to decreased efficacy of growth period (66). In general, water medication is used promotion as animals age (289) and producers mostly for metaphylaxis and treatment (66,92). wanting to have flexibility in when they market these Penicillins, tetracyclines, and sulfonamides are the hogs and avoid any concerns over withdrawal times most common antimicrobial administered through to prevent antimicrobial residues in the meat. water (66,92,93). Antimicrobial Use in Broiler Chickens Feed-grade antimicrobials are most useful for managing static or predictable health situations. Currently, no published data describe the types, Medicated diets can be administered at high-risk times amounts, or reasons for antimicrobial use in Canadian

32 national collaborating centre for infectious diseases broilers and limited data are available from the species. A good example of reporting by animal United States. Injectable antimicrobials can be used species comes from Denmark. Broiler chickens in eggs or day-old chicks. Hatchery use of injectable consumed 56 kg of the 121 tonnes (<0.001%) of antimicrobials is predominantly to control omphalitis the antimicrobials used in food-producing animals caused by gram-negative bacteria (predominantly (89). The small proportion is because Denmark has E. coli). Canadian hatchery drug use data are only a large export-based pig industry producing 1,957 available from Ontario; approximately 30% of million kg of pork and a domestic broiler industry the chicks hatched in Ontario are treated with an producing 163 million kg of chicken (89). From 2006 antimicrobial and the most common drug used was to 2007, Danish producers shifted from amoxicillin use ceftiofur followed by gentamicin (290). to macrolide and sulfonamide use due to increasing problems with amoxicillin resistance in E. coli from Beyond the hatchery, broiler chickens only receive imported chickens (89). Over this same time, a 75% antimicrobials through feed or water. As described decrease in fluoroquinolone use was attributed to in pigs, antimicrobials can be included in feed to government instructions to veterinary practitioners improve growth and/or control disease (264). about fluoroquinolone use (89). No cephalosporins Industry representatives report extensive use of were reported used in Danish poultry (89). in-feed bacitracin and virginiamycin combined with ionophores (personal communication: various Canadian nutritionists). These drugs are primarily Relationship between used for the control of coccidiosis and necrotic Antimicrobial Use in Swine enteritis. Numerous water-soluble antimicrobials or Poultry and Antimicrobial are available to producers without a veterinary Resistance prescription (Table 2). The exception to this is amoxicillin (Paracillin® SP, Intervet) (263). A challenge for any study is demonstrating causality. Cause is defined as an event, condition, Agri-Stats is a private research company that collects or characteristic that preceded the disease or the data in the United States. Their analyses show a disease event and without which the disease event marked decrease in feed-grade antimicrobial use over either would not have occurred at all or would not the past decade (165). Medications in starter and have occurred until some later time (293). While the grower diets (primarily bacitracin) fell from almost context of a single cause is a useful concept, the reality 100% of surveyed producers in 1995 to 65% in is there are often multiple causes working together 2000. Antimicrobial use in withdrawal diets (primarily to lead to an effect. In AMR, a more appropriate virginiamycin) fell from 75% to 48% over the same concept is sufficient cause. Sufficient cause is a set of period. These declines may reflect tight profit margins. minimal conditions and events that inevitably produce Producers will voluntarily remove inputs that do disease or in this case resistance. Minimal condition not increase production enough to offset their cost in this sense means that all conditions or events are (165). Declining drug use may also reflect voluntarily necessary (293). It is in situations where a cause is restrictions on antimicrobial use to satisfy consumer multifaceted or has multiple contributing sources that concerns and target premium markets or satisfy proving causality becomes increasingly difficult. production contracts (291,292). No data were found describing feed-grade antimicrobial use since 2001, Links between AMU in Swine and nor were any publications identified on therapeutic AMR in Bacteria Carried by Swine antimicrobial exposures in American broilers. There have been several articles describing European AMU data are also limited as few countries associations between AMU and AMR in swine stratify the volume of antimicrobials sold by animal (84,92,125,283,294–300). Depending on the

www.nccid.ca 33 organism and the resistance of interest, various risk use of a particular antimicrobial seems to lead to the factors for the development of AMR have been reduction of AMR is needed and warrants additional identified on swine farms. These include primarily research to attempt to identify if these negative AMU exposures, but they also reflect that stage of associations are truly due to gene incompatibility or production may influence AMR development. to try and identify ’unknown’ factors that could be contributing to this phenomenon. The expected relationship of exposure to an antimicrobial correlating to resistance to that The impacts of exposure rates on AMR development antimicrobial and other antimicrobials within that have been investigated. Rosengren et al. (299) class has been reported (125,295,298,299). But described the exposure rate of AMU and considered the use of an unrelated drug class being associated the relationship between use and resistance. with increasing resistance to a particular antimicrobial Assuming a causal relationship, this study has also been described. For example, tetracycline demonstrated that long-term use in pigs affects resistance is related to the use of sulfonamides AMR more than targeted or short-term use. Similar or aminoglycosides (299) or the use of ceftiofur results were also reported by Dunlop et al (277). can select for tetracycline resistance (283).These Supporting this concept of increased use leading associations demonstrate the likelihood of the to increased resistance, the alternative has also presence of linked genetic elements and the co- been demonstrated where the removal of use has selection of AMR (295,298,299). decreased resistance (296,301). Langlois et al. (255) demonstrated a reduction in AMR with the removal Rosengren et al. (299) demonstrated possible co- of AMU, but indicated that the reduction was less selection when they reported that macrolide use than what would have been anticipated over the was associated with resistance to chloramphenicol, study period, demonstrating that AMR can continue to streptomycin, sulfamethoxazole, and trimethoprim persist in these herds without the selective pressure sulfamethoxazole in E. coli isolates from finishing of AMU. hogs. This was surprising because E. coli is intrinsically resistant to macrolides and yet macrolide use Antibiotic free (ABF) herds have been investigated appeared to select for resistance to at least four and compared to conventional herds to elucidate other antimicrobials. Akwar et al. (295) found similar the contribution of AMU to resistance over baseline. results. Further investigation to describe any genetic From these comparisons, varying results have linkages between macrolide and other resistance been reported. Some indicated that resistance genes is warranted to more fully understand potential was more frequent on conventional farms that use repercussions of macrolide use on diverse bacterial antimicrobials than on ABF farms (302,303). These pathogens (299). findings support AMU driving resistance. But, in a different study comparing ABF herds to conventional In addition to AMU selecting for AMR, some herds, not only did the authors report that at slaughter negative associations, where AMU lead to decreased significantly moreSalmonella were isolated from the resistance, have also been reported (283,299). A carcasses of swine from ABF farms but that more possible explanation for these negative associations multidrug-resistant Salmonella were isolated from could include gene incompatibility between ABF farms (300). Since the move of some farms to resistances to certain antimicrobials. For example, ABF production is relatively recent, there is paucity of resistance genes catA1 and tetB are negatively data in this area. More research is needed to improve associated with each other (136). Another our understanding of the ecology of zoonotic bacteria explanation could be that AMU in this instance is and AMR on ABF farms and how these compare to a surrogate for some other risk factor that was not conventional farms. identified (283). A better understanding of why the

34 national collaborating centre for infectious diseases Links between AMU in Poultry and heavier birds were significantly more likely to carry AMR in Bacteria Carried by Broilers ampicillin-resistant E. coli than younger birds, despite the fact that the total E. coli shedding was lower in When looking at the impact of AMU on AMR in poultry older birds and that they had not been exposed to production, there have been several studies supporting antimicrobials (309). This indicated that as birds age that AMU leads to AMR (302,304,305). Experimental the proportion of ampicillin-resistant E. coli increased trials have demonstrated that after therapy with (309) even in the absence of any antimicrobial a variety of antimicrobials there was a significant use. In another study, that examined barns that increase in resistance levels (302,306). While these moved to ABF production that had previously used experimental trials are useful, extrapolating these fluoroquinolones, it was determined that previous use trial results to estimate in-barn selection pressure is increased the percentage of fluoroquinolone-resistant challenging because the dynamics of the resident flora Campylobacter and that this resistance continued to and historical AMU on the farm may impact the study persist in the poultry environment despite the ongoing results. Ultimately being able to use a wide variety of absence of AMU selective pressure (310). commercial farms for research purposes would be ideal since that would provide a range in management In a study comparing retail chicken from practices and exposures, but this is not always feasible organicversus intensively reared poultry, all meat had from a management, economic or practical standpoint. Campylobacter isolates resistant to nalidixic acid and erythromycin, but the resistance levels for nalidixic Due to the limitations of experimental research, acid were significantly higher in the conventional birds an alternative approach is to evaluate the impact versus the organic (311). Also, all Campylobacter of widespread AMU changes on an industry. The isolates from organically raised birds were susceptible most notable examples are the 1997 avoparcin and to ciprofloxacin (311). The results from the above 1999 broad-AGP bans in Europe. The withdrawal of studies indicate that organic or ABF production does growth promoters resulted in a significant decline in not guarantee that birds or retail meat will be free resistance to avilamycin, erythromycin, vancomycin from AMR bacteria and that there are factors other and virginiamycin in E. faecium isolated from broilers than AMU that are impacting the presence of AMR. and broiler meat (304). But most recent reports acknowledge that these initial declines have been Another example that demonstrates our limited followed by stabilized persistence of resistance. A study understanding of the ecology of AMR comes from from the United Kingdom indicated that vancomycin- work examining the impact of enrofloxacin and resistant enterococci have persisted on intensive tylosin treatment of broilers. Both enrofloxacin and broiler farms despite no avoparcin use for seven tylosin are potential therapeutic agents for E. coli years (307). Similar results have also been shown in air sacculitis (8,263). A controlled experiment Norway, where three years after the ban of avoparcin, found erythromycin resistant Campylobacter did vancomycin-resistant enterococci were still being not emerge in broilers treated with tylosin (0.53g/ detected in poultry environments (308). These data liter for three days, once or multiple times) (312). demonstrate that in commercial barn settings resistant In contrast, separate studies found fluoroquinolone strains do persist on some farms for extended periods treatment significantly increased the frequency of of time and support the arguments that husbandry resistant Campylobacter; 10 mg of enrofloxacin or practices and/or therapeutic AMU probably contribute difloxacin per bird for five days in drinking water to the persistence of AMR in these situations. (313), 40 ppm of sarafloxacin or enrofloxacin for five days (314). In both fluoroquinolone studies, Studies looking at ABF poultry production and AMR are resistant Campylobacter dominated at slaughter. also available. One study looking at ampicillin‑resistant Therefore, although macrolides and fluoroquinolone- E. coli in organically raised broilers found that older resistant Campylobacter each pose a public health

www.nccid.ca 35 hazard, the consequences to humans of therapeutic The above studies all support the fact that the fluoroquinolone use in broilers appears substantially ecology of AMR is not simplistic. There are biological greater than macrolide use. Greater consideration for factors, as well as exposure factors, that impact the effects of AMU, not only on AMR in the treated the prevalence and persistence of AMR. In some birds, but on meat contamination with resistant cases simply removing a drug exposure does not bacteria, could strengthen therapeutic guidelines always lead to a reduction in AMR, and the lack developed to mitigate AMR. of an exposure does not mean that AMR will not exist. There is still more research needed to try and The threat to public health is demonstrated by identify what other factors may be impacting AMR the development of resistance to third-generation development and/or persistence especially in the cephalosporins by Salmonella. As mentioned in absence of AMU selective pressure. Chapter 1, Canada, through its national surveillance efforts, has identified a link between AMU and AMR in chickens (66). Salmonella Heidelberg is among the Information Gaps and Challenges top five serovars isolated from human salmonellosis in Understanding the Effects of cases in Canada and the United States. Resistance to Antimicrobial Use in Livestock ceftiofur (a third-generation cephalosporin used only on Public Health in animals) among S. Heidelberg isolates is highly correlated with reduced susceptibility to ceftriaxone, Most classes of antimicrobials used in livestock a third-generation cephalosporin used exclusively in are also used in human medicine. One of the humans. Ceftiofur is used as a prophylactic agent in problems with using the same class of antimicrobials broiler chicken hatcheries to reduce losses associated in both humans and animals is that as a result of with omphalitis. Shortly after the inception of the cross‑resistance the development of resistance to a CIPARS retail component, a sharp rise in resistance particular drug within a class of antimicrobials can to ceftiofur was detected in both retail meat and result in resistance to the entire class. One class of human S. Heidelberg isolates (Figure 2)(66). When antimicrobials used in animals and not in humans first detected, CIPARS presented these data to its is the ionophores such as monensin, narasin, stakeholders. To address this public health concern, salinomycin and lasalocid, the quinoxalines, and hatcheries in Québec voluntarily stopped the use of avilamycin (316). While these drugs are not used in ceftiofur in hatching eggs and day-old chicks. This people, their use could still potentially impact AMR voluntary withdrawal was followed by an observed development through the process of co-selection. decrease in ceftiofur resistance in retail chicken Although, a particular drug may or may not be used in and human S. Heidelberg isolates (Figure 2) (66). humans, the reality is that through gene linkage and Subsequently, there has been anecdotal information transfer any antimicrobial use could ultimately have a that the use of ceftiofur in the hatcheries has been negative impact on human health. reinstituted at some level. According to CIPARS data, an increasing trend of ceftiofur resistance supports One way to try and understand the role of AMU on this return to ceftiofur use (Figure 2). These data AMR is through risk assessments. Risk assessments do show support for the correlation in trends over (RA) can be used to try to evaluate the consequences time between human S. Heidelberg resistance to to human health from the use of antimicrobials in ceftiofur and retail chicken S. Heidelberg resistance animals. Risk assessments involve the estimation to ceftiofur. While this cannot show definitive of risk for situations that cannot be measured or causality, it does warrant further investigation to gain observed and provide an interface between science a better understanding how ceftiofur use in poultry is and policy (293). The goal of a RA is to determine impacting human salmonellosis cases. a quantitative or qualitative value of risk related to a concrete situation and a recognized hazard. These

36 national collaborating centre for infectious diseases Figure 2. Resistance to ceftiofur for retail chicken E. coli, retail chicken, and human clinical S. Heidelberg isolates(315). Reproduced with permission.

assessments involve the calculation of the magnitude the bacteria the resistance was identified in, ignores of loss and the probability it will occur based on the effects of continuing the practice and the ability assumptions and data estimates that are not directly for AMR to spread to other organisms. The other testable (293). As result, RA are often inconclusive. potential biasing effect of RA is that they are generally commissioned for a reason and may be either subject Several RA have been performed to assess the to bias in the interpretation and reporting of results, impact of AMU in animals on the development of or prone to criticisms of bias. For these reasons RA AMR in humans (317–321). One of the identified may be limited in what information they can provide. limiting factors of these assessments in providing a However, in the absence of other methodologies precise estimate is the need for a better quantitative that can provide insight on the potential impact data on the rate of transmission of AMR bacteria of a particular hazard, risk assessments can be an and resistance genes between animals and humans important tool especially if the results are considered (317,319). Other limiting factors of these assessments in light of the limitations of RA. include limitation to one bacteria, antimicrobial, outcome, animal species, and antimicrobial use The alternatives to risk assessments are; reviews of (246). These factors, along with limiting the scope the literature, primary research, observational studies, of the analysis to what has already happened and to and interpretation of longitudinal data. Again, these

www.nccid.ca 37 alternatives have potential limitations such as bias, rise was beyond what was expected based on rates misinterpretation, lack of power or study size, lack of before the ban. Also, after the ban, human foodborne ability to quantify certain critical data, and the inability illness rates increased through most of Europe to control for all potential confounders and risk (328–330). When comparing the number of human factors. These methods are rarely able to put together campylobacteriosis cases after the ban in Europe the ‘whole picture’ as risk assessments attempt to do. to those in the United States (which did not have a ban), there was a significant rise in campylobacteriosis Regardless of the approach to summarizing data or cases in Europeans while at the same time in the to assessing the risk of AMU in animals on human US, there was a drop in campylobacteriosis cases by health, there is still a great deal of controversy and 30% (87,331). While some of this rise in Europe may conflicting evidence as to the actual risk. For example, have been due to the increased consumption of fresh in the case of invoking the precautionary principle chicken during this time, the extent of the increase there is a wide range of opinions as to the impact, not was in excess of what would have been predicted only on human health but to animal health and food by a change in consumption practices (332). Also, safety. In the following paragraphs several examples between 1995 and 2001 in the United States, a have been provided in an attempt to demonstrate 90% drop in Campylobacter loads in chickens was the divergence of opinion, with the ultimate goal of observed (333). The contrast between what was illustrating that this debate is far from being resolved. happening in Europe and in the United States is interesting because while Europe was banning AGP A common position is that the bans were effective in and seeing a rise in human health issues, the US achieving their goal and these proponents supported was implementing hazard analysis and critical control their position though evidence of decreased points (HACCP), increasing public awareness through rates of AMR in bacteria from animals and food education and implementing prudent use guidelines (13,304,322). But an opposing position is that policy (323), and as a result, the US subsequently saw a that invoked the ‘precautionary principle’ to ban AGP decrease in human illness. Whether these differences lacked sufficient and conclusive scientific information. are like comparing apples and oranges or relate Concerns exist that these bans may ultimately have directly to the use of antimicrobials in livestock potentially dangerous and inconsistent effects on and poultry is impossible to determine, but they animal and human health (323). There is concern contribute to the scientific debate and rhetoric around that the AGP bans have increased rates of animal AMU policy. Ideally if a similar phenomenon occurs in illness which may impact human health by increasing the future, national surveillance programs will be able the microbial load of zoonotic pathogens as well as to elucidate valid causes. increasing the need for therapeutic antimicrobial use (266,324,325)(325). In addition to increasing the In addition to the impact on human health as a result shedding of zoonotic pathogens, concerns exist that of banning AGPs, there was also an impact on animal diseased flocks can have a higher rate of processing health. Some work has indicated that the ban of errors, cuts, fecal contamination, and microbial loads certain antimicrobials for animal use had a significant (325,326). impact on animal health with an increase in necrotic enteritis in chickens and in There may be some merit in speculating that the Lawsonia intracellularis pigs (324,334). In the case of necrotic enteritis rates removal of in-feed antimicrobials may have adversely in broilers, it has been reported that morbidity rates affected public health. In the years after the European went from approximately 0% to a transient high of AGP ban, there was a rise in antimicrobial resistance 15% (323,335). In swine, Cox and Ricci indicated of hospitalized patients (327), and in the case of that it was difficult to find estimates for the impact of C. jejuni, there was a rise in resistance of several the ban on pig morbidity and mortality, but said that hundred percent in human clinical isolates (89). This

38 national collaborating centre for infectious diseases trade journals reported that from the time of the ban increase in resistance corresponded with a decreased in Denmark until 2005 there was increase in mortality use of fluoroquinolones as a result of legislation rates from 17% prior to the ban to 21% after the ban passed in 2001 (323). The reason for a rise in AMR (323,336). Probably, much of this mortality in swine despite decreased use supports the argument that was related to increased diarrhea and weight loss due the causal relationship between use and resistance to E. coli or L. intracellularis early in the post weaning is complex (323), and that other sources, including phase of production (324). Although producers environment, water, pets, other humans, etc. may experienced increased losses as a result of disease significantly influence the AMR profiles. and death immediately subsequent to the bans, after the initial surge, as a result of increasing the use of Banning Fluoroquinolone Use therapeutic antimicrobials, animal illness rates were in Poultry in the USA controlled within two to five years depending on the While the USA has not revoked labels for animal species (334,337,338). growth promotion, they have banned the use of In contrast to these findings, Wegner states, “in fluoroquinolones in poultry as a result of concerns broilers in Denmark, necrotic enteritis was at about AMR development. In the United States most a minor broiler health problem following the in 1995, the FDA approved fluoroquinolone use termination of antibiotic growth promotants” (339). in poultry for treatment of Escherichia coli and Similarly, Emborg et al. indicated that there were no Pasteurella spp. (343). Fluoroquinolones were used changes in weight gains or mortality in broilers and under veterinary prescription and delivered to the that the effects of antimicrobial growth promotant birds via water. After the launch of the product, the termination in poultry production were small and National Antimicrobial Resistance Monitoring System limited to decreased feed efficiency (340). The cost (NARMS), as a part of its regular monitoring, detected from lost feed efficiency was estimated to be offset that resistance to fluoroquinolones increased by producers’ savings on not needing to purchase from 12.9% in Campylobacter spp. to 17.6% in antimicrobials for growth promotion (341). Callesen Campylobacter jejuni and 30% in Campylobacter coli indicated that in swine there was a significant increase between 1997 and 1999 (87). In 2000, because of in treatments for diarrhea in nursery piglets and that the dramatic increase in AMR, the withdrawal of the there was some loss of productivity in weaners but no approval for fluoroquinolone use in poultry was begun real effect in finishers (342). These conclusions are (344). A quantitative risk assessment was performed in sharp contrast to the interpretations of the effect and it estimated that each year almost 10,000 of the ban on animal health and welfare described Americans would be infected with fluoroquinolone- earlier, and they demonstrate the inconsistencies of resistant Campylobacter from chicken, receive this debate and the varied interpretation of the impact fluoroquinolone treatment, and experience a of the ban. Some of these inconsistencies arise from longer duration of illness because of decreased a lack of quality animal health monitoring prior to antimicrobial effectiveness (343). The Center for the ban, while others may reflect different health Veterinary Medicine cited the following as reasons for experiences in different regions (342). taking this action: use of fluoroquinolones in poultry causes the development of fluoroquinolone-resistant Conflicting conclusions about the impact of AGP bans Campylobacter spp., this resistant Campylobacter continue to be at the forefront of debate. In some spp. is transferred to humans and is the cause instances, there has been a paradoxical increase in of the development of fluoroquinolone-resistant AMR after the ban of antimicrobial use. For example, Campylobacter spp. infections in people, and that ciprofloxacin/naladixic acid-resistantCampylobacter these infections are a hazard to human health coli isolated from swine increased significantly from (344). In several European and Asian countries a 3% in 2003 to 16% in 2004 in Denmark (89). The

www.nccid.ca 39 similar situation was experienced (340), but at this pathogen prevalence. Therefore, results of studies in time fluoroquinolones have not been banned in specific regions should certainly be considered, but these countries. development of policy or legislation based on data from potentially incomparable systems should be Final Thoughts on the Link Between approached with caution. AMU in Animals and AMR in Humans In light of data indicating that the elimination of AMU Cox and Ricci (323) suggest that the link between in feed can lead to increased bacterial contamination increased resistance in animals leading to increased of carcasses, a variety of effects of banning resistance in humans is relatively weak, based on their antimicrobials on public health must be considered. work and the work of others (159,318,345,346). Having food animal products that have minimal Others report that a link between AMU in livestock bacterial loads is critical to preventing foodborne production and increasing AMR in people is virtually illness. A part of reducing bacterial contamination certain (275, 339,347–349). Turnidge (316) has on retail meat and poultry products may include a good summary of these opposing positions. He ensuring good gut integrity and optimal animal health. contends that the main reason that the debate Since there is still a great deal to learn about the continues is that there are virtually no studies that role of antimicrobials in potentially reducing carcass accurately quantify transmission rates of antimicrobial contamination with bacteria, it is essential to evaluate resistant organisms between humans and animals. what impact, if any, the removal of antimicrobial use Although the degree of transfer is unclear, both sides would have. agree that animals can be a reservoir for AMR and that they can act as a source of amplification for Due to the wide distribution and multi-faceted nature AMR as a result of AMU. At this point, we need to of AMR, it is going to be very difficult to quantify of decide if we move forward from the debate and start the amount of AMR in humans because of AMU in controlling antimicrobial use without indisputable livestock production. Additional research examining evidence of the effects on AMR of such use (316), the causal effect of AMU in livestock on AMR in or if we continue to study the complex ecology and people, along with improved quantification of the epidemiology of AMR before intervening on AMU. transmission dynamics of AMR between people and animals, are needed but these will not be simple Conclusion tasks. When it comes to understanding and quantifying AMU in livestock, the knowledge gap grows AMR is a complex subject. The issue of AMU in exponentially. In order to be able to appreciate the livestock and its subsequent impact on human true impact of livestock AMU on AMR, a much better health will probably continue to be debated because system of collecting and reporting AMU needs to be there is conflicting evidence, personal bias, and developed. For most countries, and in the majority potentially significant political impacts on all sides of species, the unfortunate reality is that good AMU of the question. Conflicting conclusions between data are truly limited at this time. With ever changing researchers about the impact of AMU in livestock on and evolving understanding of both the molecular AMR development in humans may be the result of and global aspects of AMR ecology, there will need strong regional biases in the data since large amounts to be continually committed to modifying previous of data can come from specific regions. Differences interventions and strategies. It is also very likely that in methodology and agriculture production must also because of the complexity of AMR development and be considered when these studies are evaluated dissemination, there will never be an easy resolution to ensure that results are taken into context. Effects to contain the future development of AMR. of interventions may not be identical in regions with different management systems, climate, and

40 national collaborating centre for infectious diseases Chapter 3: Overview of Antimicrobial Resistance Surveillance or Monitoring Programs and Subsequent Policy Outcomes

Introduction actions and policies of four international organizations with mandates in human health, food safety, and Links through travel and trade make antimicrobial animal health. Although these groups largely acted in resistance an international problem requiring a the 21st century, which was after the major regulatory mix of national and international solutions. Canada changes in Europe in the 1990s, they are presented cannot address agri-food antimicrobial resistance first because they provide insight into the prevailing (AMR) without first considering the history of other global attitudes about AMR and the recommendations nations and their responses to AMR. An evaluation for a cohesive policy approach. They are presented of how international activities relate to Canada is also separately from the national regulations and required. For those readers new to the story of AMR legislations as these organizations can only issue control in food and food animals, sorting out the recommendations which member countries may history of the policies and regulations can feel like a choose to implement. convoluted journey. Many actions occurred close in time, but only some were a related sequence. Overall, The second segment describes regulations and the strategies, regulations, and policies to date have policies pertaining to veterinary drug use in Europe, predominantly focused on two particular aspects the United States, and finally Canada. Europe is of antimicrobial use (AMU) and on surveillance presented first as it has the longest history with of AMR. Regulations have aimed to improve the this issue, and many decisions there have shaped appropriateness of AMU. In Europe, this largely meant the international and North American responses. banning antimicrobial growth promoters. In contrast, Canada is presented last to allow a comparison of North America has focused on policy and regulations our veterinary drug regulations with others. The final to improve prudent AMU. Surveillance of AMR, and section describes international surveillance activities to a lesser degree AMU, is occurring in many regions in AMR and AMU. Canada is presented first with of the world. Most countries appear to recognize that a detailed description of our program followed by they lack sufficient data to make optimal decisions other noteworthy programs, which are compared and are investing in long-term programs that provide to Canada. consistent and comparable data over time and space. International Organizations’ Scope and Objectives Response to AMR in Agriculture The objectives of this chapter are to familiarize readers with the history of policies and strategies to International organizations recognize that AMR control AMR in other parts of the world to allow a transcends national boundaries. Several international sufficient evaluation of Canada’s current approach organizations have, in accordance with their and future options. Once again, the scope is limited mandates, provided recommendations to foster a to AMR as it pertains to bacteria in pigs and chickens globally-cohesive response to this threat. Most of the from farm to abattoir and processing. This chapter international activity addressing AMR has occurred does not investigate the effects of these policies in the 21st century. The following discusses the because examples of these have been discussed mandates, positions, and recommendations of the in Chapter 2. This chapter begins by describing the United Nations’ World Health Organization (WHO)

www.nccid.ca 41 and Food and Agriculture Organization (FAO), the to protect the health of consumers while ensuring World Organization for Animal Health (OIE), and fair trade practices of food (352). In the case of Codex Alimentarius. antimicrobial use and resistance, Codex largely bases its recommendations on those issued by the WHO Under the United Nations’ system, the WHO is (353). The Codex Alimentarius Commission has responsible for providing leadership on global released a code of practice to minimize and contain health matters, shaping the health research agenda, antimicrobial resistance in food. The aim of the code setting standards, articulating evidence-based policy is to provide recommendations to prevent or reduce options, providing technical support to countries, and selections of antimicrobial resistant microorganisms monitoring and assessing health trends (350). The in animals and humans through the responsible use WHO has acknowledged that the inappropriate use of antimicrobial drugs in food-producing animals. of antimicrobials has exacerbated the selection for The code provides guidance for the prudent use antimicrobial resistant organisms and in response of antimicrobials in food-animals, addressing developed the first global strategy for the containment guidelines on the prescription, application, distribution of antimicrobial resistance published in 2001 (270). and control of drugs used for treating animals, This summarized six key recommendations regarding preserving animal health, and improving animal the use of antimicrobials in food-producing animals. production (353). These are as follows: i) obligatory prescriptions for all antimicrobials used for disease control in While the mandate of Codex is limited to food, the animals; ii) in the absence of a public health safety OIE is an international organization that is responsible evaluation, terminate or rapidly phase out the use of for improving animal health worldwide (354). The antimicrobials for growth promotion if they are also OIE has outlined in its terrestrial animal health code: used for treatment of humans; iii) create national i) criteria for development and harmonization of systems to monitor antimicrobial usage in food national AMR surveillance and monitoring programs; animals; iv) introduce pre-licensing safety evaluation ii) recommendations for AMU monitoring in animals; of antimicrobials with consideration of potential iii) guidelines for responsible and prudent use of resistance to human drugs; v) monitor resistance to antimicrobials in veterinary medicine; and iv) risk identify emerging health problems and take timely assessment methodologies for assessing AMR corrective actions to protect human health; and vi) arising from AMU in animals (355). The terrestrial develop guidelines for veterinarians to reduce overuse code is published annually and is aimed to assure and misuse of antimicrobials in food animals. The the sanitary safety of international trade in terrestrial WHO regularly works in conjunction with FAO and the animals and their products. The guidelines that are OIE, which have food and animal oriented mandates, currently being developed for risk assessment aim to address this issue. to provide a transparent, objective, and scientifically defensible way for member countries to assess The agricultural arm of the United Nations, the FAO, and manage the human and animal health risks of leads international efforts to achieve food security antimicrobial resistance from the use of antimicrobials and aims to raise nutrition, improve agricultural in animals. productivity, improve the lives of rural populations, and contribute to the growth of the world economy. The World Trade Organization (WTO) recognizes The FAO provides a neutral forum for developing and both the OIE and CODEX as reference organizations. developed countries to negotiate agreements and The WTO is the only global international organization debate policy (351). Jointly established by the WHO that deals with the rules of trade between nations. and OIE, the Codex Alimentarius is an international The WTO agreement on sanitary and phytosanitary organization responsible for generating standards (SPS) measures was established in 1995. The SPS

42 national collaborating centre for infectious diseases agreement gives basic rules for food safety and i) sole therapy or one of few alternatives to treat animal and plant health standards. The agreement serious human disease and; ii) antibacterial used allows countries to set their own standards, but to treat diseases caused by organisms that may says regulations must be based on science and be transmitted via non-human sources or diseases should only be applied to the extent necessary to caused by organisms that may acquire resistance protect humans, animal or plant life or health. They genes from non-human sources. Antimicrobial classes should not arbitrarily discriminate between countries meeting criteria 1 and 2 were ranked as ‘critically with similar conditions (356). The SPS agreement important;’ antimicrobials meeting 1 or 2 were ‘highly encourages the use of transparent risk assessment important;’ and if neither criteria were met, then the practices where relevant for developing and applying antimicrobial class was deemed ‘important’ (86,362). standards for food in international trade (356,357). Hence, the risk assessment methodologies Following recommendations from this meeting, the established by both Codex and the OIE are OIE created a similar ranking of antimicrobials for recognized tools for managing international trade and their importance in treating animal diseases (362). control of AMR. The overlaps of both critical lists for human and veterinary medicine collectively provide insight to These international organizations collectively hold allow for a balance of what is needed in veterinary a global mandate to address AMR from farm to medicine while taking into account public health fork. Each organization is responsible for a distinct considerations. Australia, Canada, Japan, the United segment of the supply chain. Thus inter-organizational States, and possibly others have developed their own co‑operation has become the mainstay for most national ranking of antimicrobials for their importance of the policies and recommendations released. All in human medicine. Canada has outlined specific of these organizations have identified the need criteria for how it determines critically important for national surveillance or monitoring systems for antimicrobials (Table 3) (363). While the international antimicrobial resistance (270,358–361). The global list provides a global perspective and facilitates a diversity of animal production systems, and veterinary consistent approach between countries, the national and public health infrastructures, necessitates that lists more precisely reflect the antimicrobial needs these guidelines be general and overarching. in each country. This makes them more applicable to regulatory decisions within those countries. For Ranking of Critically Important example, Canada and the United States use their Antimicrobials respective lists for risk prioritization and assessment of which antimicrobials used in agriculture require risk In 2003, the FAO, OIE, and WHO initiated a joint management to avoid undue risk to human health, meeting to discuss issues related to antimicrobial and then apply this information to reviews of new use in agriculture and veterinary medicine, while veterinary drug applications (272,364). understanding the essential role antimicrobials play in human and animal medicine (359). The outcome was a ranking system for critically important antimicrobials (CIA) (362). These were concluded as, “antimicrobial classes that provide specific treatment or one of a limited number of treatments for serious human diseases or pathogens that cause foodborne diseases.” WHO developed a list of critically important antimicrobials based on the following two criteria:

www.nccid.ca 43 Table 3. Canada’s criteria for categorization of antimicrobials by their importance for human medicine.

Preferred option for treatment No or limited alternatives Category of serious human infections* available I – Very High Importance Yes Yes II – High Importance Yes No III – Medium Importance No No / Yes IV – Low Importance Not applicable Not applicable

*Serious infections are considered those which if left untreated would lead to significant morbidity requiring emergency care including hospitalization and/or mortality. Table taken from Categorization of Antimicrobial Drugs Based on Importance in human Medicine, Veterinary Drugs Directorate (363).

Policy, Strategy, Regulation, growth promoters from all other veterinary drugs. This resulted in prohibition of using tetracyclines and and Legislation to Address penicillins as AGP (259,260). Concurrently, European AMR in Agri-Food Europe countries made all veterinary drugs available by prescription only. In 1986, Swedish producers opted In 1963, the United Kingdom experienced an to ban all AGP to assuage consumer concerns over of multidrug-resistant Salmonella AMR, while acknowledging that the scientific evidence Typhimurium that was linked to therapeutic was incomplete (337,366). Thus, it has been over antimicrobial use in veal calves. In response to the forty years since Europe and North America initially possibility that antimicrobial use in food-producing diverged in their regulation of veterinary drugs, and animals could be causing disease in people, the over this time these differences have continued Joint Committee on the Use of Antimicrobials in to grow. Animal Husbandry and Veterinary Medicine was established and published a seminal report in 1969 The catalyst for the current global concern over (365). This report is widely referred to as the ‘Swann AMR in livestock was the emergence of community- report’ after the lead author. In it, the following acquired vancomycin-resistant enterococci (VRE) three recommendations stand out: i) antimicrobial in Europe. This raised concerns over the use of a growth promoters (AGPs) should be restricted to related glycopeptide, avoparcin, as a growth promoter antimicrobials that are not used as therapeutics in in animals (367-369). In 1995, countries began animals or people and restricted to drugs that will not to independently ban avoparcin, and in 1997 an impair the efficacy of therapeutic drugs through the EU‑wide ban was enacted (259). As described development of resistant bacteria; ii) antimicrobials more fully in Chapter 1, the pharmaceutical industry used in animals should be divided into feed (i.e. responded to the need to treat VRE by releasing a growth promoting) and therapeutic classes; and new antimicrobial under the trade name Synercid® iii) therapeutic antimicrobials should be available only (162). The active pharmaceutical ingredient in by veterinary prescription (365). Synercid® is quinupristin/dalfopristin which is related to a feed-grade antimicrobial, virginiamycin. Prior to Although the Swann report acknowledged gaps and the release of Synercid, the use of virginiamycin in uncertainties in the scientific evidence, European animals was of minimal concern because there was countries responded to its recommendations and no product from this class of antimicrobials that was separated the legislation for in-feed antimicrobial being used in human medicine (162,164).

44 national collaborating centre for infectious diseases The premise of avoiding AGPs that are related to The United States antimicrobials used in people is almost impossible to The United Sates and Canada face many similar comply with in any system that permits this type of issues regarding veterinary drug regulations. AMU. The lack of new antimicrobial discoveries has Specifically relating to antimicrobials in food-producing meant that the human pharmaceutical industry has animals, American concerns exist around the remodelled old classes of antimicrobials to address following: i) extra-label drug use (ELDU); ii) evidence- emerging problems. This situation is not limited to based risk assessment of human health risks from virginiamycin. Bambermycins were historically limited AMU in livestock; iii) non-prescription access to to use in animals, but have recently been touted as antimicrobials (commonly known as over-the-counter the “holy grail for antibiotic drug discoveries” under or OTC); and iv) use of in-feed antimicrobials for the name moenomycin, and ionophores are being growth promotion or improved productivity. The developed for topical therapy of bacterial and viral first two points are being addressed through FDA diseases under the name gramicidin (370–372). The regulations, no evidence of action was found on the limited discovery of truly novel antimicrobials means third point, and the final point has fuelled numerous that drugs previously not used in human medicine bills supporting more restrictive antimicrobial are now being used to help combat resistance issues drug legislation. that have continued to emerge.

Following the ban on avoparcin in 1997, the EU Extra-label Drug Use banned four additional AGPs in 1999. These included Extra-label drug use is the use of any drug in a way spiramycin, virginiamycin, bacitracin, and tylosin not indicated on the label. It is described in more (259). This ban did not target a specific bacterial detail under Canada, with only American specific pathogen or resistance outcome but was designed legislation presented here. In 1994, the Animal to decrease the ecological selective pressure from Medicinal Drug Use Clarification Act (AMDUCA) long-term, low-dose AMU. The EU’s policy on AMU in gave American veterinarians the flexibility to use agriculture was formally completed through the 2006 animal pharmaceuticals in situations not specifically legislation that revoked the remaining four AGP feed listed on the label providing the use occurred in the additives: monensin sodium, salinomycin sodium, context of a valid veterinary-client-patient relationship avilamycin, and flavophospholipol. The poultry (VCPR). The AMDUCA specifically excluded certain industry was granted continued access to ionophores ELDU practices. Feed-grade antimicrobials could without prescription until 2013 (259,260,324). The not be used extra-label under any circumstance. As broad-based European ban of all AGP is unique well, the FDA can impose a restriction of ELDU on compared to the response of any other country. a certain product or group of antimicrobials in food While other countries have banned individual drugs, animals. This has been applied to chloramphenicol, to our knowledge, no others have made such fluoroquinolones, and glycopeptides and, as will be sweeping changes. The European actions may be discussed, was recently considered for cephalosporins explained by the precautionary attitude to food safety, in food-producing animals (281). but the implementation of this action was almost certainly facilitated by the 1970s regulations that Risk Assessment of Human Health separated AGPs into a distinct class of antimicrobial from AMU in Food Animals inputs. Banning all AGP in North America would The FDA is addressing concerns of AMR in bacteria require changes to many aspects of veterinary drug from food animals through a multifaceted regulatory regulations. In contrast, Europe did not have to framework that includes pre-approval safety open their veterinary drug regulations to change and evaluations, post-marketing surveillance, and risk eliminate access to AGPs. management strategies. Evaluating new antimicrobial

www.nccid.ca 45 drug submissions for both safety and microbial Virginiamycin was the second antimicrobial evaluated effects on bacteria of human health concern was by the FDA for AMR risks in humans. The human embarked on in 1998 and rolled out to industry in health risk from virginiamycin use in animals and 2002 (272,373). These regulations focus on enteric the FDA-CVM risk assessment has been described bacteria and require a risk assessment approach, in Chapter 1 (164). Following release of this risk which can be based on the OIE Ad Hoc Group assessment, no regulatory action has been taken on Antimicrobial Resistance recommendations (164); possibly because other antimicrobials have (272,374,375). since replaced QDA as the most important treatment for vancomycin-resistant enterococci. The post-marketing requirements depend on the perceived risk to human and animal health and Most recently, the FDA proposed prohibiting extra- may include surveillance through the National label cephalosporin use in food-producing animals Antimicrobial Resistance Monitoring System (NARMS). (378). Ceftiofur is a third-generation cephalosporin Risk management occurs via controlling drug access. available as an injectable product for use in chickens, Antimicrobials that require veterinary supervision to pigs, and other food-animals (379). NARMS ensure appropriate use are licensed as prescription surveillance identified rising resistance to third- drugs. Other antimicrobials may be licensed as non- generation cephalosporins in Salmonella from prescription drugs. The continued option to register cattle, pigs, chickens, and turkeys and these findings new drugs as non-prescription is interesting, given the were corroborated by the Canadian Integrated new regulations provided an opportunity to decrease Program for Antimicrobial Resistance Surveillance the number of antimicrobials available without a (CIPARS) surveillance data from retail chicken veterinary prescription. The FDA may also prohibit the (66,115). The proposed prohibition cited concerns extra-label use of a drug or limit the extent of use. For that hatcheries were using ceftiofur extra-label, a example, drugs may be limited in exposure duration practice also noted by CIPARS (378,380). Following or to use in individual animals (272). an extended public comment period, with response from many agricultural sectors that restricting ELDU Through these regulations, the FDA has revoked, of cephalosporins would cause an animal welfare evaluated, and considered relabelling drugs and disease crisis, the FDA revoked the extra-label to address risks to public health from AMU in cephalosporin prohibition in November 2008. food animals. The only antimicrobial that has Evaluation of this concern continues, but if the FDA been removed from the market is water-soluble wishes to prohibit extra-label cephalosporin use, it enrofloxacin licensed for use in poultry. Enrofloxacin must re-initiate the entire regulatory processes (381). and another fluoroquinolone, sarafloxacin, were licensed in 1995 and 1996 respectively (376). As Antimicrobial Use in Food Animals to described in Chapter 2, rising rates of ciprofloxacin Improve Growth and Productivity resistant Campylobacter were identified in poultry and human clinical isolates (68,262,376). Together, In the United States, legislative bills are regularly surveillance and quantitative risk assessment results introduced to federal and state governments in were used to scientifically justify the removal of water support of restricting or banning AMU in livestock. For soluble enrofloxacin from the American market in example, bills entitled ‘Preservation of for September 2005 (8,343,376). This legislation did not Medical Treatment Act of 2009’ were submitted to apply to sarafloxacin because its manufacturer Abbott the United States Senate (Senator Edward Kennedy Laboratories voluntarily removed it from the American S.169) and House of Representatives (Rep. Louise market prior to 2000 (377). Slaughter H.R. 1549) on March 17, 2009 (382). These bills propose that new antimicrobial drug

46 national collaborating centre for infectious diseases applications be denied unless there is a reasonable Two concerns that were raised in this report, and certainty of no harm to humans due to AMR from Health Canada’s subsequent response, are pertinent non-therapeutic use of the drug. They also propose to the current discussion. The first concern was that that approvals for non-therapeutic drug use in food- Canada address ELDU. The second concern was producing animals be withdrawn two years after over Canada’s lack of action to ban the sale of drugs enactment of the Act unless safety requirements are that, based on scientific evidence, pose a risk to met. To date, such bills have not been passed, but the human health. This concern pertained specifically persistent submissions demonstrate a strong support to a non-antimicrobial drug, diethylstilbesteral, but base and the potential for AMU to become managed was also applicable to in-feed non-therapeutic AMU by legislation rather than regulations. If passed, these which had been banned in Europe the previous changes would move the United States closer to the year (385). The changes in Canada’s veterinary precautionary principle approach of the EU. drug regulations subsequent to the 1997 consensus conference and the 2000 EC audit are the focus of Canada the following section.

In Canada, the role of food safety policy and In 2002, an Expert Advisory Committee that was regulation is mandated to Health Canada and convened by the Veterinary Drug Directorate (VDD), enforcement to the Canadian Food Inspection Agency Health Canada, submitted an extensive report on (CFIA). Within Health Canada, the Veterinary Drugs “Animal Uses of Antimicrobials and the Impact Directorate (VDD) has the directive to protect human on Resistance and Human Health” (248). This and animal health and the safety of Canada’s food Committee was established in 1999 as a result of the supply with a focus on veterinary drugs administered 1997 consensus conference. In total, the Committee to food-producing animals (383). Hence, licensing of made thirty-eight recommendations, twelve of which veterinary pharmaceuticals is a federal responsibility specifically pertained to veterinary drug regulations that relates to the provincial responsibility for and five of which directed specific actions. These five regulating the sale and distribution of veterinary drugs recommendations are as follows: i) develop methods (248). Although there are is substantial differences and criteria for human health safety assessment between the Canadian provinces in their regulation of veterinary drugs with respect to antimicrobial of veterinary drugs, this document is limited to resistance; ii) define threshold levels of resistance for discussing federal regulations. post-approval surveillance and provide for appropriate In 1997, Health Canada hosted a national consensus remedial action if thresholds are surpassed, up to conference entitled ‘Agriculture’s Role in Managing and including modification of approval or suspension Antimicrobial Resistance.’ Delegates attending this of marketing; iii) develop an extra-label use policy conference called for Health Canada to address AMR that ensures this practice does not endanger human and AMU in the agri-food and aquaculture sectors health. Such a policy should include the ability to (384). This conference supported initiating AMR prohibit the extra-label use of specific drugs of critical surveillance and influenced changes to Canada’s importance to human health; iv) evaluate, register, veterinary drug use regulations. and assign a drug identification number (DIN) to all antimicrobials used in food animals in Canada, Three years after this conference, the European whether manufactured domestically or imported. Commission (EC) audited Canada’s control of This includes bulk active pharmaceutical ingredient chemical residues in animals and meat. This audit (API) products with intent to stop the direct use of was conducted to ensure Canada continued to meet APIs in food animals and; v) make all antimicrobials the consumer needs of the EU and was sweepingly used for disease treatment and control available by critical of Canada’s veterinary drug regulations (385). prescription only.

www.nccid.ca 47 In addition to these five suggestions, a Salmonella, Campylobacter, commensal E. coli and recommendation was made to conduct risk enterococci. (364). assessments of currently approved antimicrobials, including but not limited to those with a growth The VDD has post-approval marketing requirements. promotion claim, for their potential effects on human Guidance documents for industry emphasize health. This recommendation echoed the concerns surveillance for resistance to antimicrobial classes of the European Commission in 2000. In response considered critical to human medicine (364,388). to the recommended strategies from this expert This surveillance may be conducted through a Committee, Health Canada has made efforts to combination of federal programs, the most applicable address the first four of the above recommendations of which is CIPARS (364,383). However, given of the Advisory Committee. We did not identify any that critical thresholds triggering action have not activities pertaining to changing veterinary drug access been established due to their complexity, post- to prescription only or to conducting risk assessments approval surveillance is in truth actually monitoring for currently approved antimicrobials. (389). A role of the Expert Advisory Committee on Antimicrobial Risk Assessment is to consider how risk Criteria for Human Health Safety assessments may contribute to the development of Assessment of Veterinary Drugs thresholds for action. with Respect to AMR Extra-label Drug Use The VDD has established a multi-disciplinary Expert Extra-label drug use (ELDU) is the actual or intended Advisory Committee on Antimicrobial Resistance Risk use of a drug in animals in a manner that is not in Assessment with a mandate to provide advice on accordance with the approved label (285,390). For scientific methods to evaluate the human health risk example, any use that is in a species, for indications, from antimicrobial resistance (386). In particular, this at dosages, frequencies, or administration routes that Committee is focused on the validity of various risk are not on specifically stated on a product’s label are assessment methodologies for establishing thresholds ELDU. Deviation from label use creates concerns and application to drug monitoring. Over a three-year about drug residues as the appropriate withdrawal history, a major contribution from this Committee time has not been determined for the circumstances has been guidance on a classification scheme for of use. Antimicrobial resistance may be a concern if antimicrobials according to their importance in human the use alters the selective pressure on bacteria. medicine (as described above) (363,387,388). This classification is used by the VDD in new antimicrobial Extra-label drug use is an important tool for veterinary drug applications (364). medicine. Minor or exotic species have few drugs licensed for use in them, which limits labeled The VDD requires new antimicrobial drug applications treatment options (286). Likewise, less common to include information pertaining to AMR, including diseases may have limited or no label treatment applicant submitted risk assessments. These include options. Pharmaceutical companies typically seek data on the phenotypic and genotypic resistance label claims for major commodities and prevalent mechanisms in the target bacteria and the resistance pathogens; demonstrating safety and efficacy of drugs patterns expected in non-target bacteria. Applicants is costly and time consuming so labels for minor uses must consider AMR development and transmission often lack sufficient return on investment. including cross-resistance and co-selection in target pathogens, relevant foodborne pathogens, and In Canada, extra-label use occurs in broilers and commensal bacteria. There is specific focus on the pigs (personal communication; Dr. Patricia Dowling, possible effects of the antimicrobial on the flora of the Director of Canadian Global Food Animal Residue intestinal and colonic microbiota with emphasis on Avoidance Databank (CgFARAD)). The CgFARAD has

48 national collaborating centre for infectious diseases extensive data on possible ELDU in poultry because Active Pharmaceutical Ingredients the CFIA requires that veterinarians obtain a CgFARAD The Health Products and Food Branch (HPFB) have issued drug withdrawal time recommendation for been addressing concerns over the use of active all poultry exposed to ELDU drugs. Producers report pharmaceutical ingredients (API) in animals. Licensed the ELDU and withdrawal time when they ship birds establishments (i.e. pharmaceutical companies or to slaughter. In chickens, most inquiries pertain to research institutions), veterinarians, and pharmacists in-feed unlicensed drug combinations. Inquiries can import API. Some API are in dosage form, have regarding AMU in-feed at doses that are not on the demonstrated manufacturing standards that meet label or in age categories of birds that are not on the Canadian requirements, and are issued a Canadian label is less common. Swine data are less complete DIN and permitted for sale. Others are imported because abattoirs do not require a CgFARAD as bulk products for further compounding and do withdrawal recommendation. Thus the inquiries are not receive a DIN until they have been modified incomplete and more varied. To date, they have to dosage form using processes regulated by the largely pertained to therapeutic AMU to control an government. Health Canada’s greatest concern is endemic pathogen, Streptococcus suis. with bulk API that are being sold as finished products Currently, extra-label use of non-prescription drugs is for veterinary use thus bypassing manufacturing not limited to veterinarians but can be practiced by standards and controls. If importers lack good pharmacists, trainers, producers, animal owners, and manufacturing practices, these products could include other non-health care professionals. Untrained users impurities leading to human or animal toxicity or may not appreciate the risks of ELDU to public health inaccurate active ingredient concentrations. This and food safety (285,286,391). In 2002, the VDD could potentially result in residues in excess of established a committee to provide expert advice and maximum limits or inadequate levels resulting in guidance on a commissioned study entitled ‘Drug inappropriate dosing and the potential for further Use in Animals Study.’ This committee became the resistance-pressure. Inappropriate bulk API use puts ELDU Advisory Committee and released an issues public health and export markets at risk. Within the identification paper in 2004. Since then, Health HPFB, stakeholder consultation has occurred and a Canada has released a policy on ELDU, recognizing policy statement was released in 2007. The policy its importance but also recommending against ELDU specifically pertains to concerns over the sale and outside of a VCPR and for antimicrobials considered distribution of bulk API to farmers, pharmacists, feed of very high importance to human health (388). The mill operators, and veterinarians for use as dosage federal government’s jurisdiction of ELDU is limited drugs (392). The HPFB policy outlines how API because of the provincial regulation of veterinary should be handled and the appropriate regulation drug sales. This seems to have limited the VDD to that governs importation and use of API. making a recommendation, which is less enforceable than the American prohibition of ELDU for certain Own use Importation critically important antimicrobials, but does match Importation of antimicrobials without a Canadian the approach and tone of the United States. Overall, DIN by producers is another concern in Canada’s this policy aims to promote the prudent use of drugs veterinary drug regulations. The ‘own-use in food producing animals in order to minimize the loophole,’ as it has become known, is a regulatory risks to public, animal, and environmental health omission that permits ninety days of worth of a and addresses the concerns raised by the Expert pharmaceutical drug that is not licensed in Canada Committee and Advisory Committee (285). to be imported for personal use. The intent of this regulation was to allow people receiving medical

www.nccid.ca 49 care internationally to return to Canada without address this issue because it requires changes to the interruption in therapy (393). However, it is used pharmaceutical distribution system. Ethical debate by producers to import pharmaceuticals that are over veterinarians concurrently prescribing and selling either not licensed in Canada or are available more pharmaceuticals exists, and restricting antimicrobial economically elsewhere. The ability to import drugs access to prescription could be perceived as for ‘own-use’ purposes raises concerns about the supporting a veterinary monopoly on drug sales impact that these drugs may have on antimicrobial (397,398). In some jurisdictions, this has been resistance development and meat residues and addressed by limiting veterinary profit on antimicrobial toxic contaminants. sales to a pre-defined handling fee. Another challenge for limiting OTC pharmaceuticals has been ensuring Health Canada has faced opposition to changing this alternative access. In some rural areas competitor regulation. Stakeholders argue that out-of-country veterinarians may be distant and licensed pharmacists access to pharmaceuticals is the only mechanism that may not be trained in veterinary science. Our ensures pharmaceutical prices remain competitive understanding is the only avenues open to the VDD in Canada (393,394). Others have raised concerns are to re-license all antimicrobials as prescription about the VDD backlog in approving new-drug drugs, effectively passing the distribution problem submissions. They argue that closing the own-use on to the provinces, or to continue supporting its loophole puts industry at a competitive disadvantage policy statements that ELDU should be limited to due to delayed product access. An estimate from VCPR and limit approvals of new applications for the Canadian Animal Health Institute suggests that non‑prescription antimicrobials. about one-third of all veterinary drugs (not only antimicrobials) used in Canada are drugs imported by Comparison of International Veterinary producers for their own use (380), but to date there Drug Regulations and Policy are limited data on the effects that these importations may have on food safety or the economic effects on In summary, Canada has some distinct differences producers and the pharmaceutical industry. This issue in veterinary drug regulations from Europe and the remains at the consultation level. The task force that United States. First, in Europe all veterinary AMU was put in place to examine this issue has called for must be accompanied by a prescription. In contrast, further study before drawing any conclusions (394). both Canada (excluding Quebec) and the United States permit non-prescription sales and use of Limiting Antimicrobial Access through antimicrobials. Second, European authorities do Prescription-Only Licenses not allow antimicrobials to be included in animal feeds without a veterinary prescription and then use Continued access to non-prescription antimicrobials is is only to address a disease indication rather than counterproductive to prudent AMU guidelines, which improve growth or productivity. In contrast, there are based on the premise that AMU should occur are currently no feed-grade antimicrobials licensed within the confines of a VCPR to ensure evidence- for use in pigs or chickens in Canada that require a based decisions (395). It also could have a negative veterinary prescription when used according to the impact on animal health based on the lack of a label (263,264). Label indications can include a list of veterinarian in the decision-making process and the specific diseases as well as a growth promotion claim. potential for inadequate or contraindicated therapies. In Canada, feed-grade antimicrobials may be included Over-the-counter (OTC) access to antimicrobials also in diets in an extra-label manner if accompanied by complicates AMU data collection (281,396). The a veterinary prescription. Although non-prescription sale of veterinary pharmaceuticals is under provincial in-feed AMU is permitted in the United States, jurisdiction and Quebec has a prescription only extra‑label use is prohibited (281). system (248). Other provinces have struggled to

50 national collaborating centre for infectious diseases Superficially, the differences between Europe and and most have faced challenges in responding to North America may appear minor; but they belie recommendations for AMU data collection. a fundamentally different approach to food safety policy. Canada and the United States have committed Basic Premises of AMR Surveillance to evidence-based policy while Europe has employed Surveillance is a continuous and systematic process the precautionary principle in its legal statutes. of collecting, analyzing, interpreting, and disseminating The European Environmental Agency has defined descriptive information for the purposes of and clarified the precautionary principle as, “the understanding and describing health issues (402). Precautionary Principle provides justification for public Over time, surveillance can be used to identify trends policy actions in situations of scientific uncertainty and emerging situations. Surveillance can detect and ignorance, where there may be a need to act and report on the incidence or prevalence of health in order to avoid, or reduce, potentially serious or outcomes and identify at-risk groups. Surveillance irreversible threats to health or the environment, data may be useful for assessing the effects of using an appropriate level of scientific evidence, and interventions applied to the issue of concern. There taking into account the likely pros and cons of action is often a balance between the desire for the best and inaction” (399). The disparate approaches to information and feasible data collection (402). The regulating AMU in livestock mean that North America ideal national system should include monitoring both and Europe tend to interpret risk prioritization, animal and human use as well as resistance levels assessment, and management differently. Ideally, risk in bacterial species from animals, animal derived assessment, evidence-based science, cost-benefit and foods, and humans. Several factors are important to precautionary approaches should be combined to consider when designing an integrated monitoring provide a balanced decision-making process (400). system, including: the main purpose of the system, As scientific research and observational studies help the reservoir of interest, the bacterial species, and the clarify the links between people, food, and animals, antimicrobial agents to include. our approaches to managing AMR and veterinary AMU may become increasingly similar. As a result of needing long-term cooperation from participants, and due to the breadth of surveillance Surveillance and Monitoring of in time and geography, surveillance is generally less detailed and precise than research projects. Antimicrobial Resistance and Use However, surveillance and research can complement There is international consensus that countries should each other. If through surveillance a particular area conduct AMR surveillance in animals and/or food to of interest or concern is detected, then research monitor trends, provide a basis for the development can be used to investigate the issue in more of national policies, and assess interventions. depth and detail. Conversely, research studies can Antimicrobial use data are essential to understand the identify new issues that may benefit from formal causes of AMR. The WHO, FAO, and OIE recommend ongoing surveillance. that countries collect veterinary AMU data (359). At a minimum, these data should include the national Surveillance can be active or passive (403). Active use of antimicrobial agents in kilograms of active surveillance employs statistically valid sample ingredient on an annual basis and be reported using collection to obtain unbiased data from a targeted the Anatomical Therapeutic Classification system area or group. It must be implemented consistently (ATC). When possible, data should be stratified by across groups and over time. There is a need for animal species (359,401). Many countries have ongoing contact with the participants in order to made great progress in conducting AMR surveillance be able to collect specific data from the identified population in a consistent manner. It may involve

www.nccid.ca 51 the use of sentinel sites that act on behalf of surveillance of clinical isolates is used as only one the surveillance system to provide the required component of an AMR agri-food surveillance system. information. Active surveillance requires substantial Surveillance programs must take all of the relative financial and human resources. Passive surveillance is strengths and weaknesses of passive and active less demanding on human and financial resources. In data collection from animals, food, and people into passive surveillance, the data or samples often arise consideration, along with the objectives and resources from submissions to a lab, clinic, hospital, etc., and available, to determine the most appropriate program are subsequently provided to the surveillance system design. Each piece can provide information on using a standardized protocol. In passive surveillance, different populations, and therefore, studying both the surveillance program has no influence on presents the most complete picture. sample collection. Surveillance from farm to fork is useful for assessing Both active and passive surveillance can provide the impact of AMU in livestock and poultry production useful information. Passive surveillance is more prone on AMR throughout the food production chain. to bias than active surveillance (402,403). People Farm level AMU and AMR surveillance allows seeking treatment could have differences in their considerations of what drug are used and how they infecting pathogens compared to people with mild impact the AMR patterns on the farm. Collecting symptoms that do not seek treatment. In food animal samples at abattoir can provide information about AMR, passive data typically represent clinical isolates changes in AMR patterns between what is detected while active data often represent healthy individuals. on farm and what is being detected in the processing These clinical isolates may have different rates and plant. Depending on the stage of processing that patterns of resistance than isolates of the same these samples are taken at and how they are taken, bacterial species obtained from healthy animals. this may allow for assessment of the effectiveness of This may be due to linkages between virulence and HACCP programs, cross contamination, or changes in resistance gene, differences between commensal intestinal microbial flora as a result of transport and/ and pathogenic strains of a bacterial species, and or stress in the animals. Abattoir surveillance is the therapeutic drug exposure (26,48). This bias is easiest point to ensure samples are representative amplified in passive surveillance of clinical isolates of the livestock population and unbiased. Between from animals because producers incur laboratory slaughter and retail, the microbial load, resistance expenses. Diagnostic submissions are often only rates, and resistance patterns can again change. made for severe or non-responsive disease outbreaks, So, retail surveillance provides the best estimate of thereby creating a tendency to receive more highly human exposure to resistant organisms. A challenge resistant bacteria (404). Conversely, utilizing samples of interpreting retail surveillance is incomplete from unrelated mandatory monitoring programs can information identifying a product’s source. Knowing if artificially increase the number of submission from a a product is domestic and where it came from within certain species or region. the country or if it is imported would obviously assist with the interpretation of data collected at all points of Passive surveillance of AMR in bacteria from clinically the surveillance program. ill animals increases the likelihood of detecting emerging resistance, as this is a form of targeted In summary, the ‘farm-to-fork’ approach is useful for surveillance. It does not reflect the probability of understanding the transmission of resistance through human exposure to resistant bacteria because only the food chain and identifying potential areas for healthy animals enter the food chain. While both interventions and areas requiring further investigation. healthy and sick animals harbour resistant bacteria, In future research and surveillance, the farm-to-fork the patterns, frequencies and genetic basis for concept should be expanded to foodborne disease resistance differ (26,136). For these reasons, passive in humans. This is currently being attempted outside

52 national collaborating centre for infectious diseases of AMR surveillance programs via source attribution iv) allow accurate international comparisons with projects (96,405) but to our knowledge, no country other countries that use similar surveillance systems. is attempting to monitor the effect of AMR on clinical The several components of CIPARS (Figure 3) outcomes of foodborne disease or the proportion of are harmonized to monitor temporal and regional resistant foodborne infections that occur in individuals trends in the prevalence and patterns of AMR across taking antimicrobials prior to infection. regions, bacterial species, and hosts. Results of CIPARS surveillance are published in annual reports, National AMR and AMU Monitoring and results of detailed studies are published in peer and Surveillance Programs reviewed journals. There are many national AMR monitoring and The human component of CIPARS involves passive surveillance programs. These programs are surveillance of Salmonella isolates from clinical challenging to catalogue and many have not cases. Salmonella isolates are sent from provincial published their methodologies in peer reviewed public health laboratories and reference laboratories literature. Websites and annual reports were across the country to the National Microbiology reviewed for methodological information, but were Laboratory for phage typing and antimicrobial often incomplete. Summarizing all of the identified susceptibility testing. As Salmonella is a reportable programs would have been fraught with errors by disease in humans, these isolates should represent omission and somewhat redundant (406). The the vast majority of clinically diagnosed cases. following section highlights surveillance programs Clinical Salmonella isolates from animals are also as they relate to pigs and chicken and their meat tested. These originate from veterinarian or producer and evaluates their relevance to Canada. We have submissions to veterinary diagnostic laboratories. In selected the programs from the United States animals, Salmonella is not reportable and coverage because Canada was designed to harmonize with between provinces is variable. this program, Europe because they have been instrumental in establishing methodologies and In agri-food, surveillance is conducted in beef, ensuring ongoing prioritization of surveillance, and chicken, and pork, but only chicken and pork are Japan because it was the only program identified described. The retail surveillance component was outside of Canada that uses on-farm sampling, initiated in 2002 and provides data on antimicrobial and the only well described program outside North resistance in Salmonella, Campylobacter, and America and Europe. Enterococcus from raw chicken (skin on wings and legs), and generic E. coli from pork (chops) (Figure 2, Canada Table 4). Weekly samples are submitted from retail stores. Stores are selected by a stratified sampling The Canadian Integrated Program for Antimicrobial scheme which randomly selects census divisions, Resistance Surveillance (CIPARS) was established weighted by the population of each of the provinces. in 2002 by Health Canada (66). This is a national The abattoir component isolates bacteria from swine program that collects, integrates, analyzes, and and poultry cecal contents. The unit of concern is the communicates trends in antimicrobial use and bacterial isolate. and generic are resistance in select species of enteric bacteria from Salmonella E. coli isolated. The sampling design is a two-stage sampling. humans, animals, and meat across Canada. The Each commodity is handled separately. The first stage goals of CIPARS are to: i) use a unified approach to randomly selects slaughterhouses by a probability monitor trends in AMR and AMU in humans and that is proportional to their annual slaughter volume. animals; ii) generate timely reports; iii) generate The second stage is a systematic selection of animals data to facilitate the assessment of the public on the slaughter line, where the number of samples health impact of AMU in people and livestock; and taken per plant is proportional to their slaughter

www.nccid.ca 53 Figure 3. Components of the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS)

volume and evenly distributed over the year. The not readily available from a single source in Canada farm surveillance component was initiated in 2003 or the United States. Use data for pigs are obtained and the national sample collection in swine began in through farm surveillance. Insight into AMU in other 2006. Resistance is monitored in E. coli, Salmonella, commodities currently occurs through collaborative and Enterococcus from near market weight pigs. research projects. Recently, antimicrobial distribution The farm program relies on voluntary participation data have been provided by the Canadian Animal of veterinarians and producers across the five major Health Institute. These data will provide a context for pork producing provinces in Canada. This component interpreting livestock AMU data generated through involves approximately 100 swine farms under the research and farm surveillance (66). supervision of twenty-six veterinary clinics. CIPARS has consistently, and continues, to expand Antimicrobial use data are currently collected in to include more commodities, bacterial species, and people and pigs. Human drug use data are obtained geographical regions within Canada (Figure 4). As through Intercontinental Medical Statistics (IMS) data CIPARS expands, it will continue to act as a research and describe oral human antimicrobial consumption platform to investigate AMR and as a critical source at the community pharmacy level. Data are computed for gaining insight into emerging trends in AMR and using DDD from dispensed prescription data. As more AMU over time. fully described in Chapter 2, animal drug use data are

54 national collaborating centre for infectious diseases Figure 4. Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) Expansion Timeline.

• Established CIPARS 2002 • Commenced Passive Animal Component

• Commenced Human Clinical Component 2003 • Commenced Retail Component (Ontario, Quebec)

2004 • Expanded retail component to include Saskatchewan

2005 • Commenced Farm Component

2006 • Expanded retail component to include British Columbia

2007

2008 • Expanded retail component to include the Maritimes

2009

United States products through the USDA’s Food Safety and Inspection Service (FSIS) Pathogen Reduction: Hazard In 1996, the National Antimicrobial Resistance Analysis Critical Control Point (PR/HACCP) testing Monitoring System (NARMS) was established by the program (87,407) (Table 4). NARMS differs from Food and Drug Administration’s Center for Veterinary CIPARS by rolling its sampling focus through the Medicine (FDACVM) in collaboration with the United livestock commodities so evaluating results for trends States Department of Agriculture (USDA), and the is more difficult. Center for Disease Control and Prevention (CDC). Within the CDC, NARMS’s primary purpose is to The United States does not currently collect any AMR monitor antimicrobial resistance among foodborne data from animals on farms. A pilot program called enteric bacteria isolated from humans. All fifty states Collaboration in Animal Health and Food Safety forward samples of Salmonella, Listeria, and E. coli Epidemiology (CAHFSE) was run in swine from 2003 O157 to NARMS for antimicrobial susceptibility to 2005 (73). From the beginning, this program testing, and ten FoodNet states have been was designed to only run a few years followed participating in Campylobacter surveillance (87). by an evaluation period. American studies have Salmonella are collected from clinical cases in sick recognized that an on-farm surveillance component animals. In agri-food, Salmonella, Campylobacter, is one of the few feasible ways to collect AMU E. Coli, and Enterococcus are monitored. Retail data (281,396,408). No information was found samples are collected from meat obtained from pertaining to the potential re-initiation in swine or grocery stores, and abattoir specimens are collected expansion of farm surveillance or pilot projects in from carcass rinsates, carcass swabs, and ground

www.nccid.ca 55 other commodities. The United States describes and foods for susceptibility testing. Considering that AMU through surveys conducted by the National extensive harmonization in surveillance has occurred Animal Health Monitoring System (NAHMS) program. across European countries, and that a single report These surveys rotate between commodities and summarizes both the results and methodologies target appropriate regions of the country to achieve of individual country’s programs for AMR data from representative data for that industry. Commercial food and animals, we felt a detailed description of swine production was last targeted in 2006 and each European country’s surveillance program was commercial poultry 2004. A small enterprise study redundant (97,360,361). Instead, select national that covered both poultry and swine was conducted programs are described to highlight similarities and in 2007 (409). differences from Canada. Denmark was selected as the longest-running and most comprehensive AMR Europe and AMU surveillance program in the world. Norway Antimicrobial resistance is monitored in most was selected as an example of a comprehensive countries within Europe. A survey performed in program that is representative of Northern Europe. 1998 outlined the methodologies of 12 countries Both of these programs have been in place for over in the European Union (EU). At that time, the most a decade. Many of the more recently developed frequent bacterial group tested was Salmonella European programs are less comprehensive but may (410). The European Antimicrobial Resistance still be in the development stages. Surveillance System (EARSS) monitors resistance in human isolates for a variety of bacterium including Denmark E. coli and Enterococcus (151). Results from these Denmark established the world’s first systematic bacteria in particular are of importance due to their and continuous monitoring program in 1995 potential foodborne connection. Participating EARSS (89,322,411). The Danish Antimicrobial Resistance laboratories within each country collect data obtained Monitoring and Research Program (DANMAP) from routine susceptibility testing from invasive examines representative bacterial isolates from isolates of these bacterial species along with patient animals, foods, and humans in Denmark. Isolates information such as age, sex, birth date, and level include zoonotic and indicator bacteria (Table 4). of care. These data are then provided to EARSS Sampling occurs in food animals at abattoirs and from the participatory nations. There are currently through diagnostic submissions. Cecal contents of thirty‑one European nations who participate in EARSS. pigs and cloacal swabs of broilers are obtained and Data provided to EARSS are reviewed by experts susceptibility testing is carried out for Salmonella, before publication in annual reports. This allows Campylobacter, Escherichia coli, and Enterococcus for a more thorough representation of the current faecium/faecalis. Salmonella isolates collected status of antimicrobial resistance within Europe given from systematic random sampling from diagnostic resistance does not obey national boundaries. submissions to the Danish Veterinary Laboratory and the laboratory run by the Federation of Danish The new Zoonoses Monitoring Directive was adopted Pig Producers and Slaughterhouses are also tested. by the European Food Safety Authority (EFSA) Isolates are also included from submissions to the in 2003 to improve the comparability of data of National Food Institute. Sampling of predetermined member countries and to consistently monitor AMR foodstuffs from retail outlets and wholesalers also (97). Data from 2005 onward are reported based occurs. The foods sampled include both Danish and on the new directive. These data include AMR in imported foods, and Salmonella, Campylobacter, Salmonella, Campylobacter, Enterococcus, and E. coli. E. coli, and Enterococcus are tested. Bacterial isolates are obtained from humans, animals,

56 national collaborating centre for infectious diseases Antimicrobial use data in people are available Institute. Campylobacter is cultured from samples electronically from pharmacy sales (89). Data on collected at slaughter plants. One isolate per farm is animal use are also available electronically through included. The NORM program obtains human isolates pharmacy sales data. Veterinarians can sell from clinical specimens. to farmers but profits are limited to 5%. Therefore, most antimicrobials are sold on prescriptions. The In Norway, all antimicrobials intended for human Danish Plant Directorate monitors the consumption use are prescription and sold through pharmacies. of in-feed antimicrobials which can only be sold at Therefore, the human use data presented include feed mills in the form of premixes. Producers of total sales of antimicrobials for humans in Norway. premixes are required to report quantities of active The unit of measurement for human antimicrobial ingredients used. This provides consumption data use is defined daily doses (DDD), reflecting the but no information on the recipient animal species usage of the Anatomical Therapeutic Chemical (ATC)/ (89). These limitations were addressed by the DDD system. In Norway veterinary antimicrobials VETSTAT program, which was established in 2001 intended for domestic animals and farmed fish for to continuously monitor the use of all prescription therapeutic use are available through prescription only medicines in animals at the individual herd level and only dispensed through pharmacies. Medicated (412). Veterinarians are required by law to report the feeds have to be prescribed by veterinarians and sale of medicines to a central database. Information produced by feed mills and are only available for submitted includes the identity of the farm, receiving farmed fish. Given the small size of herds/flocks medicine, species of animal, age group, and reason in Norway, livestock are treated with antimicrobial for prescription. agents, prescribed by veterinarians, through drinking water or injection. The reporting of sales of veterinary Norway drugs is mandatory and, therefore, the number of items sold per year, drug formulations, strengths, The Norwegian AMR surveillance program (NORM) and package sizes are able to be obtained. Drugs was established in 1999 to monitor resistance are classified using the Anatomical Therapeutic in human pathogens and the veterinary arm Chemical for Veterinary medicinal products (ATCvet) (NORM‑VET) was established in 2000. An action classification system and presented as the kg of active plan developed by the Norwegian Ministry of Health substance sold in the country. Data are not stratified and Social Affairs described the need to address by species (79). antimicrobial resistance at a national level and emphasized the importance of ongoing surveillance Japan and monitoring of both human and animal sectors to aid in controlling antimicrobial resistance. The The Japanese Veterinary Antimicrobial Resistance NORM-VET program rotates through the food-animal Monitoring Program (JVARM) was established in commodities with a particular emphasis on one 1999. The objectives of JVARM are to monitor species per year. In the target commodity, commensal antimicrobial use and resistance amongst zoonotic E. coli and Enterococcus spp. are described. Chickens and indicator bacteria from healthy animals and were last targeted in 2006 and pigs in 2004. Four pathogens amongst diseased animals. Zoonotic enteropathogenic bacteria are monitored in animals (Salmonella and Campylobacter) and indicator and people annually: Salmonella, Campylobacter, (Escherichia coli and Enterococcus) bacterial isolates Yersinia, and Shigella (79). Salmonella from all are obtained from healthy animal (cattle, pigs, food-animal species are obtained during clinical broilers, and layers) fecal samples. The JVARM was examinations or necropsies at the National Veterinary the only program identified that collected samples

www.nccid.ca 57 from farms. Six samples are collected per prefecture chicken, and beef. In 2003, intestines of chicken, (region) annually with a limit of one sample per swine, and cattle were collected from slaughter (419). farm. Antimicrobial use data are acquired from A study from South Africa was conducted to aid in pharmaceutical companies which produce and the establishment of an integrated AMR monitoring import antimicrobials for animals. The annual weight program. The study was performed to make in kilograms of the active ingredient of approved recommendations for a practical and sustainable antimicrobials used in animals is collected. This only monitoring program that could provide information includes therapeutic AMU in animals (413–418). on a national scale (420). Australia currently does not have a national AMR monitoring or surveillance Studies and Pilot Projects program. However, the Joint Expert Technical Many countries have not met WHO and OIE Advisory Committee on Antibiotic Resistance recommendations to implement national AMR (JETACAR) has made a recommendation to establish surveillance or monitoring programs. In some, studies an AMR surveillance program which will follow or pilot projects have evaluated AMR. A surveillance OIE recommendations (421). In other countries, system pilot was implemented for Salmonella spp. research studies have been conducted. The following in Mexico in 2002 through to August 2005. Active references provide evidence that research in AMR in surveillance began in 2002 integrating samples food animals is occurring on every continent except from ill and asymptomatic persons and retail pork, Antarctica (66,77,97,115,419,422–427).

Table 4. Comparison of National Integrated AMR and AMU surveillance programs in Canada, United States, Denmark, Norway, and Japan.

Human Agri-food Pig Chicken

Surveillance Initiation Diagnostic Diagnostic AMU AMU Farm Abattoir Retail Farm Abattoir Retail Programs Year Samples Samples

Canada 2002 S Yes S † S, Ec,En S,Ec Ec – S,Ec S,C,Ec,En

USA* 1996 S,C,En Yes S † – S,C,Ec,En S,C,Ec,En – S,C,Ec,En S,C,Ec,En

Denmark 1995 S,C Yes S Yes – S,C,Ec,En S,C,Ec,En – S,C,Ec,En S,C,Ec,En

Norway * 1999 S,C Yes S,C Yes – C,Ec,En – – C,Ec,En –

Japan 1999 ** Yes S,C Yes S,C,Ec,En – – S,C,Ec,En – –

(C) Campylobacter (S) Salmonella (Ec) Escherichia coli (En) Enterococcus * Surveillance or Monitoring Program rotates between species annually for data collection. ** Information unavailable. Does not imply the program does not perform type of monitoring but rather information has not been found within the scope of this paper. † Agricultural AMU data are obtained through several different methods, such as studies and national distribution data. – Monitor AMR in animals and humans but methodologies are unclear. No differentiation made between active monitoring from a retail or abattoir program or diagnostic submissions. Note: Information lacking within this chart does not mean the program does not perform such monitoring but rather information has not been found within the scope of the literature reviewed for this paper.

58 national collaborating centre for infectious diseases International Comparisons species. These data are of minimal use and are not available in Canada because of privacy regulations International surveillance programs have become for pharmaceutical corporations (281,396,408). increasingly harmonized over the last decade. The Danish VETSTAT program is a census style Many of the differences in sample collection farm‑level data collection system that inventories the and susceptibility testing are being overcome, national AMU (412). This program is detailed and which makes data comparisons more valid. The world-renowned. However, it cannot be applied to described programs differ in the regularity of their Canada for at least three reasons. First, in Denmark, sampling schemes (Table 4). The CIPARS collects a all AMU is prescription only and largely occurs predetermined number of isolates, for each studied through pharmacies. This facilitates drug tracking and bacterium, from each commodity every year (66). allows validation of the farm-level data. Second, the Most other programs rotate their focus to a particular VETSTAT system is mandatory while Canada would commodity each year with or without a base level require a voluntary program. Denmark appears to of sampling across all commodities (97,407). The have different privacy regulations than Canada which CIPARS approach helps to identify changing trends in facilitate regulated data collection. But even beyond resistance over time. It also makes random variation these, operating the VETSTAT program is simplified by due to chance appear less important. For example, the structure of the livestock industry. The beef, dairy, CIPARS presents data trends and the ‘noise’ around and poultry sectors are relatively small and although resistance estimates is obvious. However, if data were the pork sector is large, it is integrated with producer collected sporadically, this noise could be considered co-operatives as the owners (428). This makes representative of reality. Although the CIPARS implementing and enforcing farm-to-fork food safety approach of regular sampling is more expensive from systems in Demark much easier because producers a laboratory perspective, it may allow efficiencies have a unified and influential voice in negotiations. in labour and program management. Effective The final reason the Danish VETSTAT system is not relationships are established with sample collectors applicable to Canada is that Canada does not possess and once trained, minimal interaction is required. the pharmaceutical industry infrastructure that enables Most integrated programs collect human clinical electronic data collection. isolates along with food-animal isolates from Canada’s AMU data collection system most closely abattoirs. Retail sampling is relatively common while mirrors the pilot program run by CAHFSE in the only Canada and Japan collect data and samples United States, but the CAHFSE pilot program ceased from farms (415). The merits of on-farm AMR data operations in 2005 (73). As evidenced by the have been discussed and largely relate to avoiding discussed veterinary drug regulations, substantial ecological bias between farm-level AMU data and differences exist between North America and abattoir-level AMR data, as well as the ability to Europe. We expect that a North America AMU look at management factors beyond AMU for their surveillance approach will emerge with minor influence on AMR. There are currently no other viable modifications to account for Canadian and American sources of valid AMU data in Canada, although the differences (408). This will benefit both countries possibilities of using surveys or data extrapolation as harmonized AMR surveillance already occurs. In continue to be evaluated. The main benefit of contrast, harmonization with existing European AMU such alternative AMU methods would be cost and surveillance is not realistic. The greatest issue that labour savings. we foresee for AMU and AMR surveillance in Canada Other countries have also struggled to collect valid is financial sustainability. Continued commitment and useful AMU data. Many European countries from the federal government is needed to ensure report sales volumes which are not stratified by the long-term viability of this world-class program.

www.nccid.ca 59 A weakness of this report is an inability to describe or Numerous concerns were raised about the validity compare the financial costs of national surveillance of these premises (429,430). These included: What programs. An economic estimation of the costs to determines a safe threshold? Should thresholds the Danish livestock industry from the AGP ban has identify resistance frequencies where public health been published, but did not extend to considering is initially affected, based on the premise that the cost of DANMAP or VETSTAT (341). The lack of interventions will reduce resistance, or should the information of cost efficiency of surveillance systems threshold be lowered to ensure that limiting further is an important information gap for decision-makers. increases is sufficient to protect public health? Should resistance be monitored in food animals, food, or The surveillance programs described would be more human cases? And should it account for resistance appropriately referred to as monitoring programs. A in pathogenic bacteria or sentinel bacteria? Who is monitoring system is an ongoing effort to describe responsible for the surveillance and its costs? And disease in a population. Surveillance is distinguished what actions should be taken when a threshold is from monitoring by having predetermined actions exceeded: increased monitoring, restricted use, or that occur when data indicate disease prevalence or complete cessation of use? incidence has risen above a threshold (403). The importance of antimicrobials for human medicine is These are a few of the questions that have hindered only one component required to establish thresholds regulators’ abilities to establish action thresholds beyond which the risk to public health from AMR in for AMR and that require consensus from scientists food animals is deemed unacceptable. The second and stakeholders for progress. These concerns piece is the likelihood of humans being affected by and questions are by no means limited to the the resistance elements in animals. In 1999, the United States but pertain to all countries attempting FDA proposed to categorize antimicrobials according to understand and address AMR and AMU in to the likelihood of human exposure to resistant food animals. bacteria from food animals that are either human pathogens or may transfer resistance elements to Conclusion human pathogens. This would involve considering Even though North America has based, and four likelihoods: i) that use in food animals will induce continues to base, regulatory changes on scientific resistance in bacteria; ii) that food-producing animals evidence, determining the appropriate time, sufficient will promote such resistance; iii) that resistant bacteria evidence and appropriate response to scientific will be transmitted to people; and iv) that transfer evidence is influenced by political pressures from will result in the loss of available human antimicrobial public health authorities, the agriculture industry, the therapies (429). To our knowledge this categorization pharmaceutical industry, trading partners, and the has not been released by the FDA or any other public. What seems insufficient to some often seems regulatory body. too drastic to others. Establishing action thresholds In this same document, the FDA proposed that these for regulations is extremely difficult and potentially two categorization schemes could be combined fraught with significant resistance from either side of to establish and monitor thresholds for AMR. Such the debate. There is a continued need for surveillance thresholds would be based on two premises. First, activities that can monitor trends over time in both that a regulatory agency could determine a threshold AMU and AMR for humans and animals to help of resistance that would adequately protect public provide the critical data that are needed to assist health, and second, that the regulatory agency has policy makers in their decision-making process. the ability to detect when that threshold is reached.

60 national collaborating centre for infectious diseases Chapter 4: Agricultural and Agri-Food Interventions to Reduce the Impact of AMR Bacteria in Pigs and Chickens on Human Health

Introduction Chicken and Pig Production and Pressures to decrease antimicrobial use (AMU) in the Broiler and Swine Industries meat animal production are being prompted by public health concerns, consumer demands, and Basics of Chicken and Pig Production narrowing profit margins (11,291,431). Canada’s The term ‘broiler chicken’ refers to birds raised for regulatory agencies are addressing international meat. Broiler producers receive day-old chicks from recommendations and standards (269,359). The the hatchery. These birds are raised as a flock using livestock industry is also facing recommendations all-in-all-out management which means that all chicks from national and international groups to eliminate arrive together, are raised together and are marketed unnecessary AMU and to decrease their reliance together. Depending on the target market, birds are on antimicrobials by improving management and finished between 1.75 and 2.2 kg and generally increasing the use of antimicrobial alternatives. range from 34 and 42 days of age. Although the Some recommendations are specific, such as the birds are managed as a single group and remain in requirements imposed by fast food chains on their the same barn for their lifespan, they are managed in suppliers, while others give generic guidelines such phases. Each phase lasts approximately 14 days and as emphasizing prevention of infectious diseases to progresses from the starter phase, through the grower avoid AMU (122,291,395,432,433). and finisher phase, to the withdrawal phase. Disease pressures vary between phases and are greatest early Scope and Objectives in life. At each phase change, the birds’ diets are This chapter is written for professionals in human altered and feed medications or coccidiostats may medicine and public health who have minimal to also be changed (personal communication: Dr. Tom no background in agriculture. It aims to inform these Ingles, Poultry Health Services, Airdrie, Alberta). professionals about industry-led initiatives in pigs and chickens that mitigate foodborne AMR risks. It also In North America, pigs are also managed in phases, describes alternative inputs or management practices but progression between phases typically entails that are available to producers to improve animal physical movement of the pigs. The suckling phase health including vaccines, competitive exclusion extends from birth until weaning. Pigs are weaned strategies, and biosecurity practices. It provides between 15 and 30 days, with most herds weaning examples rather than an exhaustive catalogue of all pigs slightly less than three weeks (126,409). alternatives and does not quantify the extent that Weaning marks the beginning of the nursery phase. each are used. Practices that control pathogens Piglets may be moved to a separate pen in the same on-farm or bacterial contamination of meat during room as sows but are more commonly moved to slaughter and processing with no plausible influence separate rooms or even sites. The nursery phase on the prevalence of resistant bacteria are excluded. is associated with increased disease risk because stressors, including mixing and diet changes, occur concurrently with declining maternal immunity. Pigs generally remain in the nursery phase until they are

www.nccid.ca 61 6 to 10 weeks of age (average, 61.8 days; S, 0.6) vertically coordinated. While few corporations control (409). Movement to the grow-finish phase completes the majority of slaughter, processing and distribution the production cycle. Pigs remain in this phase of chicken, and these corporations typically own or until marketed or selected for the breeding herd. In have strategic alliances with hatcheries, independent Canada, pigs are typically marketed at 110 to 115 kg farms raise the broilers on a production contract with live weight and are generally between 24 and 30 the processor. Feed mills are generally independent weeks old (66). of both the producers and processors (441) (personal communications: Dr. Stewart Ritchie, Industry Background Canadian Poultry Consultants and Dr. Agnes Agunos, Canada produces over a million metric tonnes of Public Health Agency of Canada). chicken on 2,000 farms annually. Most of this chicken In Canada, the swine industry is not supply is retained for domestic consumption while 15% managed. Although the last three years have seen is exported. This makes Canada the 13th largest a contraction in the industry, this contraction follows global chicken producer and the 7th largest exporter twenty years of substantial growth. The expansion (although our exports amount to less than 5% of the of the Canadian swine industry was accompanied global leaders; Brazil and the United States) (434– by industry consolidation to capture economies of 436). In contrast, Canada produces a considerable scale. The number of herds decreased, while herd proportion of the world’s pork; ranking among the size increased and large corporate producers became five largest producers in the world and accounting established. In some instances, there is vertical for 17% of the world’s exports. In 2007, 31 million integration with single corporations owning multiple pigs were produced with one-third exported live. The or all aspects of production including feed mills, pigs remaining 21 million pigs resulted in slightly less than and slaughtering facilities. But much of the industry 2 million tonnes of pork, of which 55% was exported remains segmented, particularly in comparison with (435,437,438). Despite Canadians consuming the American industry (444). slightly more chicken than pork (2008 average per capita consumption: Chicken, 11.2 kg; Pork, 9.7 kg Vertical integration, or the lack of it, has implications (439), our pork industry is far larger than our chicken for AMU decisions. Integrated companies can industry because it is export based. consider decisions from numerous perspectives, and the costs incurred in one division may be sufficiently Canada’s poultry industry is supply managed. This is offset in another to justify their incurrence (445,446). a marketing system that regulates domestic chicken These operations may have better production data, production and imports. It matches demand to supply ability to track the effect of decisions, and specialized thereby ensuring that there is a consistent national staff, which could all influence the scientific and market with stable commodity prices. Production is economic rigour applied to AMU decisions. The allocated to farms based on the amount of quota lack of vertical integration in the Canadian industry, they own. Only producers that own quota can raise particularly when animals change production more than 300 birds annually and sell them to phases and ownership, also affects AMU decisions. processors at the industry set price (440–442). This Hatcheries may treat eggs differently from breeder has protected the chicken industry from much of flocks with a known versus unknown health status, the market volatility experienced in the pork sector. and may make different AMU decisions for domestic Vertical integration is the term describing a single versus imported eggs. In the swine industry, some corporation owning all, or most, of the steps in a producers purchase weanling pigs and raise them production chain. This business model is pervasive to market weight. Again, AMU may differ in herds in much of the poultry industry worldwide (443). In purchasing from a single supplier with a known-health Canada, the poultry industry has been described as status versus multiple suppliers.

62 national collaborating centre for infectious diseases Large producers and corporate farms that own HACCP: On the Farm and multiple barns make AMU decisions that affect many animals. For example, in 2006, 40% of American At Slaughter farms used pre-weaning antimicrobials in feed but Hazard Analysis Critical Control Point (HACCP) is a only 10% of pigs produced were exposed (409). food safety management system that enables the Thus, 60% did not use pre-weaning antimicrobials food industry to pre-empt problems rather than rely and 90% of pigs were not exposed at weaning. on end product testing. HACCP consists of six generic This example shows that industry consolidation can steps. These systematically apply science to control positively affect AMU when large producers decide and document the safety of a food product. Since to limit or discontinue AMU. Supply chains can inception in the 1960s, this generic system has been also affect AMU decisions. For example, numerous effectively applied to a wide-range of food processing international fast-food chains impose the National facilities (453–455). Chicken Council Animal Welfare Guidelines on their poultry suppliers across North America (The Chicken The HACCP system begins with a hazard analysis: Farmers of Canada’s recently released Animal Care hazards are characterized as physical, chemical, or Guidelines may supersede these in Canada in microbiological. Critical control points (CCP) are then the future). Under this and the related Canadian identified for each hazard, which are points where an programs, diseases indicative of poor welfare, action could prevent, eliminate, or reduce the hazard including mortality and lameness, require immediate to an acceptable level. The third step establishes a euthanasia, veterinary advice, and appropriate therapy critical limit which, if exceeded, triggers a response. (447–449). The final three steps of HACCP are establish a monitoring system, establish and implement Supply management may have implications for AMU corrective actions when monitoring identifies a decisions. Supply management provides financial problem with a CCP, and establish verification stability to chicken producers, relative to producers of procedures that ensure you do what you say and say export-based commodities (namely pork and beef) what you do. Records and documentation are crucial (441). This may contribute to an industry stance on components of the HACCP program and are legal antimicrobial use that has financial consequences documents (454). but consumer and/or political appeal. Examples include an industry-mandated recommendation The HACCP programs are often implemented in against active pharmaceutical ingredient (API) use processing plants to reduce carcass contamination and the own-use importation of drugs. In contrast, the and improve food safety (455,456). We found no Canadian pork industry is export-based and drug-use evidence that AMR is an identified hazard in abattoirs. decisions may be influenced by importing nations’ This is intuitive because controlling resistance and customers’ standards for antimicrobial use or inherently means controlling the bacterial host. resistance (450,451). As such, the Canadian Pork Furthermore, critical limits for a ‘safe’ prevalence Council has stated in its Canadian Quality Assurance of resistance do not exist. National authorities and Policy on Drug use that own-use importation of surveillance programs have struggled to establish drugs is not permitted, but that API use may occur thresholds and subsequent appropriate responses to providing that producers do not use bulk API and that exceeding such thresholds (See Chapter 3). Hence, the final dosage form is accompanied by a veterinary any private HACCP plan developed to control AMR prescription and has been identity tested (452). would struggle to identify sufficient scientific evidence for setting a ceiling for AMR levels. We speculate that if AMR became a trade issue, abattoirs might attempt to modify HACCP programs to address AMR hazards,

www.nccid.ca 63 but we would expect control would be targeted at exceeding a threshold, which could subsequently be further minimizing bacterial contamination rather than moved into low-risk product streams, such as further attempting to control resistance elements. processed and pre-cooked meats. Such an approach has been taken with Salmonella and Campylobacter The HACCP approach can be applied to systems control in Europe (64,459,460). beyond food processing. The Canadian Food Inspection Agency (CFIA) has released a Food Safety Enhancement Program that requires a HACCP plan On-Farm Food Safety Programs for all federally registered food establishments, The Canadian Pork Council’s Quality including hatcheries (457). Twelve hatcheries are Assurance (CQA) and the Chicken currently registered across Canada. This plan must address hatching egg quality, and the CCP addresses Farmers of Canada’s Safe, Safer, risks from imported and domestic eggs, as well Safest Programs as the handling and quality of the hatched chicks. A lack of data describing AMU in agriculture has been Antimicrobial use can be considered as a chemical a major stumbling block for understanding AMR. In and biological hazard (personal communications, Canada, producer-led organizations in swine and Dr. Agnes Agunos, Public Health Agency of Canada). poultry administer on-farm food safety programs that collect data on antimicrobial drug use (284,458). On-farm food safety programs (OFFS) can be The ‘Safe, Safer, Safest’ program was initiated by HACCP-based (284,458). They are not true HACCP the Chicken Farmers of Canada in 1998, and the systems because biological processes are inherently Canadian Pork Council implemented the Canadian more variable and less controllable than industrial Quality Assurance (CQA) program in 2001. These processes. The Canadian programs described next programs are designed to ensure best management provide a general HACCP plan that is applied to all practices in biosecurity, disease control, sanitation, producers. In contrast, a true HACCP program is drug handling, and residue avoidance. tailored to each process. Rather than using CCP, OFFS programs identify good production practices (GPP) Producers are required to record AMU data. The that might minimize the risk of the hazard at any AMU data are not compiled or analyzed across the point in production, not just at a specific point. Finally, industry. The primary objective of recording AMU data OFFS programs are not HACCP programs because is to mitigate risk from antimicrobial drug residues, while the OFFS requires a plan, with compliance and so these programs focus their description of ensured through external audits and verification, AMU near to market. In pigs, AMU through feed is they lack monitored thresholds at CCP (284,458). described through the entire production cycle and This prevents processors from knowing the entry through injection and water after weaning. In poultry contamination levels from which they must act to the AMU data are limited to the two weeks closest achieve their CCP levels. to slaughter. The AMU data do not accurately capture exposure dose, duration or drug combinations. In Canadian OFFS programs cannot yet feasibly address our opinion, the most valuable data from these AMR because intervention points and thresholds must programs for addressing AMR is the information be science-based. More research is needed on how on producer decisions and attitudes towards AMU. and where resistance elements enter flocks/herds, If compiled, these answers could facilitate the the transmission dynamics once they are present, development of effective programs by describing and the factors that allow persistence. These same producer knowledge uptake and compliance with questions also require investigation at the industry OFFS programs. Although Canada’s OFFS programs level. However, it is foreseeable that OFFS programs were not designed specifically to control AMR, they could identify batches or flocks with AMR frequencies do provide an on-farm link to inform producers about

64 national collaborating centre for infectious diseases risks from AMU. The existence and survival of these by treatment protocols. These guidelines should be a programs demonstrates an industry-wide willingness valuable resource for veterinarians, but their influence to respond to regulatory and consumer concerns over is unknown because their uptake and use is not food safety. tracked. More specifically, the uptake of treatment protocols is unmeasured and may change over time Prudent Antimicrobial Use if these guidelines are not flexible and kept current. Critics have raised concerns that, although these Guidelines protocols are written for veterinarians, they may serve Prudent use, judicious use, or antimicrobial as a ‘therapeutic recipe book’ for producers, thereby stewardship involves reducing inappropriate AMU undermining efforts to bolster VCPR. This, too, would and selecting the optimal drug, dose, and duration be interesting to monitor. when use is necessary to ultimately reduce the emergence of AMR (461). A necessary tool to ensure Focusing guidelines on veterinarians may be valuable prudent use is education, thus the standardized AMR for initiating discussions about prudent AMU amongst education for Canadian veterinary students that was veterinarians and between veterinarians and clients, jointly developed by the Canadian Veterinary Medical but does not address the fact that most antimicrobials Association (CVMA) and the Canadian Committee on in Canada are available without a veterinary Antibiotic Resistance (CCAR) in 2007 should improve prescription. Administering antimicrobials within a AMU by future veterinarians (462). In veterinary VCPR is ideal because the veterinarian understands medicine, several organizations have designed animal health as well as the herd’s disease status prudent use guidelines which have been summarized and so can design treatment regimens to maximize by Weese (395). These consistently recommend efficacy while minimizing bacterial resistance. avoiding unnecessary AMU. They also emphasize Veterinarians are trained to account for complex the importance of basing necessary use decisions on interactions between microbe pharmacodynamics susceptibility testing, and they suggest that when an and antimicrobial pharmacokinetics through their antimicrobial is required that the narrowest spectrum knowledge of physiology, anatomy, and disease drug is administered for the shortest time possible. pathology (463,464). However, non-prescription These guidelines all support the notion that AMU antimicrobials are available in Canada and the should involve veterinary advice (268). For example, challenges involved in limiting antimicrobials to the CVMA has stated that all antimicrobials, including prescription only were discussed in Chapter 3. So, non-prescription antimicrobials, should be used failing to target non-veterinarians in prudent AMU within the confines of a veterinarian-client-patient guidelines is an important oversight in Canada. relationship (VCPR) (390). Only one education program for producers pertaining Published AMU recommendations target veterinarians to appropriate antimicrobial drug use was identified. because of the premise that AMU should occur Ten years ago, the Ontario Ministry of Agriculture, within a VCPR. Again, using the CVMA as an example, Food and Rural Affairs (OMAFRA) developed a the recently released Prudent Use Guidelines swine medications course as a proactive response 2008 for beef cattle, dairy cattle, poultry, and swine to address the possibility that certification would be recommend that veterinarians: i) take efforts to required to purchase non-prescription antimicrobials. design a health management program to prevent and Veterinarians delivered this program to producers. reduce disease; ii) look for antimicrobial alternatives; Such certification was never required and the program iii) prescribe all antimicrobials within a valid VCPR; was discontinued after Ontario Pork took over its and iv) select and use antimicrobials appropriately operation. In the initial five years, producer uptake (390). Detailed recommendations are accompanied of the program was good, but it is now available only on an ad hoc basis through OMAFRA swine

www.nccid.ca 65 experts (personal communication: Dr. Janet Alsop, interventions that improve health and resultantly OMAFRA). No other programs for producers, and no minimize AMU. programs for nutritionists, were identified in Canada. Considering that no feed-grade antimicrobials, all but Alternatives to Antimicrobials one water antimicrobial, and over one-third of the injectable antimicrobials licensed for use in pigs and Vaccines chickens in Canada are non‑prescription drugs (263), Antimicrobial resistance is most likely to emerge the number of prudent use guidelines targeted at and persist when AMU involves low doses, mass veterinarians versus producers seems unbalanced. medication, and long exposure durations (268–271). Producers and animal nutritionists should have Some antimicrobial classes that are critically important access to training on which practices elevate the risk in human therapy are also used as feed additives to of antimicrobial residues at slaughter, antimicrobial control disease in pigs and chickens. The following resistance in bacteria carried by food animals, and examples relate to macrolide use to control ileitis approaches to prudent antimicrobial use. Such (causative agent, Lawsonia intracellularis) in pigs training should emphasize the value of seeking and virginiamycin use to control bacterial enteritis veterinary advice for antimicrobial use decisions rather (causative agent, Clostridium perfringens) in chickens than attempt to train the producer or nutritionist in (86,100,465,466). If expert opinion is correct and the optimal antimicrobial decision. AMR can in part be mitigated by addressing long- Therapeutic recommendations within AMU guidelines term, low-dose antimicrobial exposures, reducing the often overshadow the crucial point that prudent use of these drugs should alleviate selective pressures AMU demands that animal health be optimized for AMR in bacteria carried by pigs and chickens. through husbandry (much like the reduce component Three recently developed vaccines allow non- of reduce-reuse-recycle is often overlooked). antimicrobial control of these endemic conditions. Veterinarians can play an important role in designing These vaccines were selected as examples of health programs. In order to do this effectively, advancements in animal health that positively affect veterinarians must continually update their knowledge public health. of disease prevention, therapeutics, and AMR trends Ileitis causes chronic diarrhea in pigs between 6 and to ensure the most appropriate use of antimicrobials 20 weeks of age. It is endemic in pigs worldwide, (390). Effective health programs that include cannot be eradicated from herds, and until recently , biosecurity, good hygiene, and improved was extremely difficult to diagnosis. The combination management should prevent disease and thereby of diagnostic limitations and financial losses has reduce the need for antimicrobials. Veterinarians must led to widespread AMU in feed for disease control. also seek current continuing education to ensure The most common prophylactic regimens include their ability to design and implement evidence-based tiamulin, tylosin, chlortetracycline, or lincomycin health programs (390). Unless Canada licenses all fed continuously (100,465). In 2002, an avirulent antimicrobials as prescription drugs, building and live vaccine (Enterosol®, Boehringer Ingelheim establishing trust in VCPR is the only insurance that Vetmedica, Inc.) was released on the Canadian producers will seek veterinary advice for all AMU, market (467). This vaccine is administered through regardless of availability. Continuing to build such drinking water and significantly reduces disease relationships may ultimately foster efforts to capture prevalence and severity (465,468). For financial people’s imagination that through AMU stewardship reasons, this product is used more extensively in they can refuse (do not use), reduce, and potentially grow-finish pigs in Europe and more commonly affect AMR development and dissemination (268). in breeding animals in Canada (468). The CIPARS The following sections describe examples of sentinel herds in 2007 reported 76% of sow herds

66 national collaborating centre for infectious diseases supplying sentinel grow-finish sites were positive for and five viral vaccines licensed for use in pigs (263). ileitis and 26% vaccinated. In the grow-finish herds, Describing these products would be redundant, but 66% reported a positive status and 17% reported we want to emphasize that the selected examples vaccinating (469). are not the only vaccines with great effects on animal health. All vaccine use should decrease AMU, In broilers, bacterial enteritis is among the most either by directly preventing bacterial disease or by prevalent and financially costly diseases. An preventing viral disease and secondary bacterial overgrowth of C. perfringens causes disease infections. The National Veterinary Institute in symptoms ranging from wet litter to death. In Denmark described the top 12 diseases diagnosed in feed, bacitracin or virginiamycin, combined with pigs in 2007 (474). Canada has licensed vaccines to a coccidiostat, is used to control this syndrome control all of these except swine dysentery (causative and these products account for much of the AMU agents Brachyspira hyodysenteriae and B. pilosicoli) in broilers (165). The coccidiostat is necessary (263). Thus, advancements in vaccine technology because coccidia damage the gut and predispose have undoubtedly affected AMU, and therefore, AMR. birds to more severe disease (466,466,470). Both Future advances will likely include new vaccines to coccidia and C. perfringens are endemic in poultry. control food safety hazards, such as the licensed Two vaccines have been developed to control Salmonella vaccines in chickens and pigs (263). these pathogens. Conversely, it would be amiss to leave the impression that all important disease can be controlled with Coccidiosis vaccines are licensed in Canada (263). currently available vaccines. Pathogens such as avian These live oocyst vaccines are sprayed on chicks pathogenic and at the hatchery and stimulate a mucosal immune E. coli, Staphylococcus, Pseudomonas are important in broilers and have no effective response (471). Vaccine efficacy depends on vaccines. Other non-antimicrobial interventions are establishing high levels of vaccine-strain oocysts in also not available. This demonstrates the industry’s the barn early in the birds’ lives combined with good continued need for efficacious antimicrobials, and litter management. Coccidiosis vaccines alone are their continued reliance on antimicrobial availability. often insufficient to manage gut-health. Prophylactic in-feed antimicrobials cannot be used in conjunction with this live vaccine so, if vaccine failure occurs, Competitive Exclusion Strategies the subsequent coccidiosis and bacterial enteritis Competitive exclusion strategies (CES) encompass a outbreaks are severe. This can be resolved by broad range of products that manipulate gut bacteria. concurrent use of a bacterial enteritis vaccine in the As categories, these include competitive exclusion broiler breeders (466,472). A conditionally licensed products, probiotics, and prebiotics. Most are oral vaccine (NetVax®, Intervet Schering-Plough Animal products. Competitive exclusion (CE) and probiotics Health) is available in the United States and can be are live bacterial or yeast preparations that moderate accessed in Canada via an emergency biological the normal flora, while prebiotics are inert non- release permit (473). These products are important digestible additives that support beneficial bacteria. advancements because they prevent disease, the Competitive exclusion strategies are so named coccidiosis vaccine can diminish the virulence of field because CE or probiotics can be used synergistically strains, and both are compatible with competitive with prebiotics (268,475,476). The objective of exclusion strategies. These characteristics should these products is to shift the gut ecology away speed industry adoption resulting in public health from pathogens by displacing them with beneficial spin offs. commensal bacteria (475).

Canada has three bacterial and ten viral vaccines Neonatal animals are born with an immature licensed for use in chickens and thirteen bacterial intestinal flora. Competitive exclusion products are

www.nccid.ca 67 live obligate and facultative anaerobic bacteria, There are at least two reasons for the regulatory typically originating from the intestinal contents of restrictions on undifferentiated CE and probiotic healthy adults. They are administered in the first products. Health Canada’s Veterinary Drugs days of life. This expedites establishment of the Directorate (VDD) uses the same registration climax population; a stable intestinal microflora process for pharmaceuticals and natural health that is more resistant to invasion from pathogens products. Although this is being reviewed, it is (335,475). Competitive exclusion technology has difficult to register natural health products because particular application in chickens. While pigs are many requirements are difficult to achieve with exposed to maternal flora, chickens are hatched in biological processes (483). Delays in licensing clean environments and raised separate from breeder veterinary pharmaceuticals are a serious concern flocks. Establishing the climax population takes six for producers and the pharmaceutical industry, and weeks, which is the majority of a modern broiler’s life, natural health products are only one area requiring and is predominantly influenced by the environment immediate attention to maintain the Canadian (477,478). livestock industry’s competitiveness internationally (484). Yet, amendments to VDD regulation may not Probiotics are live bacterial cultures that differ from result in market approval for undifferentiated bacterial CE products because they are fed continuously products. Undifferentiated cultures may pose an AMR (478). They can be monostrain, multistrain (of one risk if they possess resistance elements. These could species), or multispecies combinations and are be rapidly disseminated from a single source to many primarily composed of gram-positive bacteria (479). commercial flocks/herds (482). An experimental Unlike competitive exclusion products, probiotics are study with a porcine-derived undifferentiated CE not always derived from the animal species they are culture found higher levels of tetracycline and administered to (475). The mechanisms of probiotics streptomycin resistance in E. coli from exposed pigs are not completely understood and likely vary with compared to controls (485). Undifferentiated CE different organisms. Factors such as organic acid products are derived from mature animals, which production, bacteriocin production, and stimulation of generally carry resistant bacteria, so these results the immune system have been demonstrated, with were not unexpected. Ideally, future preparations will an impact on colonization or infection by pathogenic distinguish between bacteria that are non‑therapeutic bacteria or parasites (480). and commonly carry resistance elements, such as and therapeutic bacteria that rarely carry Undifferentiated CE and probiotic products are E. coli, resistance genes, such as lactic acid bacteria. If derived from intestinal content. These are essentially achieved with minimal impact on efficacy, the risk of crude preparations of bacteria from healthy AMR from these products could be diminished. animals. The bacterial content is not identified or quantified. Early studies suggested these may be The European Union requires antimicrobial resistance more efficacious than defined cultures, but this susceptibility testing of undifferentiated products may simply reflect the infancy of this field’s ability (479). This approach is not foolproof. Traditional to identify optimal mixtures of beneficial bacteria culture-based techniques cannot demonstrate (481) Undifferentiated but quality-controlled and freedom of resistance because resistance genes pathogen‑free products are available in Europe can be silent (carried but not expressed) and but prohibited in Canada and the United States culture‑based techniques test a small, and potentially (364,479,482). In North America, cultures must be unrepresentative, sample of the bacteria in the composed of identified bacteria demonstrated to be product. Molecular testing for resistance genes beneficial (478). This limits the range of products addresses these problems but will not detect novel available in North America. resistance mechanisms. But together phenotype and

68 national collaborating centre for infectious diseases genotype testing can provide some assurance that beneficial bacteria and exclude pathogens. Neonatal concerning resistance types are not being widely animals with naïve flora are now commonly studied disseminated through undifferentiated cultures. to minimize uncontrolled confounding and decrease variability. Beyond study design, disappointing results Studies of CE and probiotics products have had with live bacterial products have been attributed to wide-ranging results, both beneficial and detrimental. challenges in maintaining an exogenous population of Although this promising research field may some bacteria without continuous administration. This may day help address the pharmaceutical void created be difficult to overcome as the balance of intestinal by removing in-feed antimicrobials, advancements in microflora appears to not only be species and gut basic knowledge along with improved study designs location specific but to have important variability and more precise outcomes are needed before between individuals (454,475,478,481,495). inconsistent findings are overcome. Serious concerns exist over the use of enterococci in CE products Food safety may be improved by CES if these due to their propensity to carry resistance genes. prevent the colonization of animals with foodborne As discussed above, other bacterial species may pathogens. A variety of studies in pigs and chickens be more promising. A cautious regulatory approach have found these products can affect colonization should help to ensure that these products ameliorate or shedding of Salmonella and Campylobacter, but rather than contribute to agri-food AMR. results are preliminary, variable, and are preparation and pathogen specific. (496,497). Commercial Prebiotics are a dietary supplement that are available application will require continued research. However, to microbes and provide limiting nutrients to the this research field holds great potential because these intestinal mucosa but provide no direct nutritional products can concurrently address animal and human benefit to the animal host (335,475,486). Prebiotics health challenges. are commonly used in people, while uptake in agriculture has been limited due to expense (475). Bacteriophages Research from humans and animals suggest various prebiotics can modulate the immune system, Another area that may have promise in the future is the use of bacteriophages, viruses that infect neutralize pathogenic enterotoxins, and bind E. coli bacterial cells. There are two forms of bacteriophage, and Salmonella (471,475,487). Prebiotics are not restricted to antimicrobial-free production because the temperate and lytic. Temperate bacteriophages effects complement in-feed antimicrobials (488,489). infect, but do not damage, bacterial cells and are a Therefore, these can be considered an antimicrobial potential mechanism for transmission of virulence alternative or simply an advancement in human and and antimicrobial resistance genes. Accordingly, they animal intestinal management. are not useful therapeutically. Lytic bacteriophages, in contrast, kill infected cells. Some bacteriophages Studies of CES have shown variable results on have broad-spectrum activity while others only infect animal productivity and health (489,490), which a narrow range of bacterial species, or even strains along with expense, has limited commercial uptake. within a species. In addition to the potential for Early studies sought to improve growth and did efficacy, lytic bacteriophages are appealing because not evaluate the microbial ecosystem. But Europe’s of their safety. Bacteriophages are unable to infect experience following in-feed antimicrobial bans mammalian cells and therefore are non-pathogenic made it clear that in-feed antimicrobials concurrently to animals. This field is relatively young and ongoing suppressed disease while improving productivity safety evaluations are needed. However, temperate (491–494). Thus, recent efforts have focused on bacteriophages are classified as ‘generally regarded as more specific objectives such as manipulating the safe’ (GRAS) by the FDA, are classified as Biosafety microbial population to optimize niche dominance of Level 1 microorganisms (as with Lactobacillus spp.)

www.nccid.ca 69 and have fewer regulatory hurdles to clear, and In broilers, this occurs during brooding, and in pigs, have minimal to no evidence of ability to convert post‑weaning (100,471,478,510). to temperate forms. The potential efficacy of lytic bacteriophages is of great interest and has been Commercial operations almost exclusively raise discussed for decades, however objective data has a single commodity, of one genetic background, been lacking until recently. that are similar in age (note: single-site swine operations still have multiple ages in a barn) in a Bacteriophages could be used for the elimination common airspace. This elevates the risk of infectious of bacteria in or on animals, or in the environment. disease. Risk is determined by both the severity Intensive research on bacteriophages in swine and of the outcome and the probability of occurrence poultry has been fairly recent, but preliminary data (374). Because of their size, both are magnified in are promising. Bacteriophages with in vitro efficacy intensive livestock operations. This risk is addressed against swine pathogens such as ETEC, Salmonella, by practices that control enzootic disease and block and Streptococcus suis have been identified epizootic outbreaks. Good management practices (498–502). In vivo efficacy has been reported as to control endemic disease are relevant because well, with certain bacteriophages being effective at they decrease the need for antimicrobials and may moderating the course of experimentally-induced be extrapolated to controlling AMR within barns. ETEC (E. coli F4) diarrhea (503). Bacteriophages Nutritional advancements are presented as an with in vitro efficacy against important pathogens in example. Disease exclusion strategies are relevant poultry such as Salmonella and E. coli have been for preventing devastating disease and resultant identified (504,505). Bacteriophage therapy has been therapeutic drug use. Biosecurity principles are shown to reduce Salmonella and Campylobacter presented as an example and may have application shedding in broiler chickens (506–509). Research is for precluding entrance of novel resistance still needed on the rate and extent that bacteria will determinants. develop resistance to lytic phages. Nutrition and Feed While not acting directly against AMR, bacteriophages could have an indirect impact by reducing disease Animal nutrition is constantly advancing to optimize and concurrent need for antimicrobials. Further, genetic potential and protect health. In both chickens bacteriophages could be used against multidrug- and pigs, advancements in high quality starter diets resistant pathogens such as MRSA. This is a field that have eased the transition to solid food. Anorexic is receiving increasing attention and might constitute a animals can experience gastric stasis which places useful adjunctive therapeutic option in future years. them at increased risk for pathogen colonization (100,101,476). Ensuring chicks and piglets get onto feed as soon as possible after brooding/weaning Best Management Practices supports the gastrointestinal flora through this There is no ‘magic bullet’ that eliminates the need challenging period for the immune system. for AMU in food-animal production. European Union In the late 1990s, the North American swine industry producers identified a return to ‘good management’ initiated a management system known as segregated as the most effective intervention following early weaning. Pigs were weaned as young as antimicrobial growth promoter bans. Likewise, the fourteen days and moved to ultra-clean off-site North American experience in antimicrobial-free nurseries. Separating piglets and sows was effective production emphasizes barn hygiene, stocking in containing many respiratory pathogens to the density, ventilation, and for chickens lighting, and breeding herd, but it created nutritional challenges litter management. Particular attention must be paid for feeding immature pigs. The transition from milk to when animals are immunologically compromised.

70 national collaborating centre for infectious diseases a plant-based diet in young animals is facilitated by actions to implement that plan. Biosecurity is a risk high quality animal protein, which in North America management tool, much like insurance. In the case of is typically derived from milk or blood (spray-dried on-farm biosecurity, producers incur costs up-front to plasma) products. Using quality ingredients, palatable minimize future risks. Many biosecurity protocols also diet forms (i.e. crumble), managing feeders and apply to bio-containment, which in this context is the waterers, and occasionally offering creep feed before control, eradication, or prevention, of new incurrence weaning have all worked to get weaned pigs onto of infectious agents. feed quickly. By eating and minimizing gastric stasis, a healthy gut flora is supported and enteric diseases Biosecurity can be applied to farms, regions, or are prevented. The standard industry weaning age nations. Protocols are implemented to control has increased since the 1990s, but these advances pathogens with sufficient consequences or probability continue to influence nutrition in the nursery (100). of incursion (i.e. risk) to justify the expense and effort. This is significant since nursery production uses more These protocols address animal, human, , and antimicrobials than the other production phases. vector borne risks. Sanitation is not truly biosecurity, (92,93,282,409). but is often included because it is a barrier to disease between groups of animals in a flock/herd. Poultry nutritionists have modified diets to minimize In Canada, on-farm biosecurity protocols vary from the risk of bacterial enteritis (337,366,511). This was non existent to extremely stringent (476,512-514). stimulated by European experience following the antimicrobial growth promoter bans when wheat- Control of animal movement is essential for disease based diets fuelled necrotic enteritis outbreaks control. Many swine barns and all broiler operations (493). Along with adjustments to the carbohydrate are closed to live animals after they fill. Many swine source, feed grind is now balanced for health and broiler operations prefer to receive animals from (larger) and productivity (smaller), and whole a single source. Within barns, an animal movement grains are occasionally included to stimulate gizzard pattern known as ‘all-in-all-out’ is commonly used. development. Other advancements have included This management approach batches animals by increased use of synthetic amino acids, a focus on fat age, moves them as a group, and prevents contact quality, and inclusion of enzymes to facilitate digestion between batches. When combined with sanitation, of non-starch polysaccharides. Canadian nutritionists this helps to prevent aerosol and fecal-oral disease employ these techniques resulting in an industry with transmission between groups of animals (100). All-in- decreased risk of enteric disease. all-out is inherently more effective in poultry than pigs because hatcheries supply chicks that have never had Nutritional advances are relevant to AMR because physical contact with the breeder herd. Additionally, they support health and decrease reliance on AMU. the entire poultry barn is emptied between groups, These advances also support the healthy intestinal while swine barns often employ all-in-all-out by room flora, and like CES, help preclude colonization with within a barn. All-in-all-out is less effective without enteric pathogens. Finally, this section has relevance sanitation. Although it prevents the spread of disease for addressing endemic resistance problems by between animals through direct contact, barns should emphasizing the benefits that can arise when new be emptied of litter/manure, washed with detergent, technologies are applied to old husbandry questions. disinfected, and allowed a dry down time between groups for optimal efficacy (515). Roughly three- Biosecurity quarters of American swine producers use all-in-all- Biosecurity is the collective measures taken to out management and the uptake of this practice has ensure security from exposure to harmful biological increased from approximately half of producers in agents. Thus biosecurity is both the plan and the 2000 (409).

www.nccid.ca 71 In theory, preventing bird/pig contact between groups animals. Upon entry, visitors may be required to could help to control AMR. A study investigating shower and/or change clothing. This minimizes the AMR in Campylobacter found pig herds with all- risk of people acting as a fomite. An experimental in-all-out management had lower odds of multiple study demonstrated that enterotoxigenic E. coli drug resistance than herds with partial all-in-all-out can be transmitted between groups of pigs by or continuous flow management (516). Although handlers despite hand washing and outer-clothing western Canadian field studies examiningE. coli and change between groups. Transmission did not Campylobacter from grow-finish pigs failed to find a occur when handlers showered between groups relationship between pig flow and AMR, this could be (518). Downtime and showering between farms attributed to insufficient power. Conversely, a lack of is important, as a British study found flocks using relationship might exist in the grow-finish production ‘thinning’ (split marketing heavy birds and leaving phase because pigs enter the phase with high lighter birds to continue growing) are at increased risk resistance levels (84,299). of Campylobacter infection. The risk is attributed to the catchers who move from flock to flock (519). In broilers, fluoroquinolone resistance inE. coli has been traced to vertical transmission from the breeder People can act as a source of infectious disease to flock, most likely through hatchery contamination birds/pigs, as presumably occurred in the recent and re-infection (517). (Note: vertical disease H1N1 ( strain) infected swine farm in transmission is the spread of disease from one Alberta (520). No studies were identified that generation to its progeny, typically from mother to investigated the rate of transmission of resistant offspring. It is used to differentiate from disease bacteria from healthy people to chickens/pigs under transmission within a group of contemporary normal contact conditions. This is another area of animals which is termed horizontal transmission.) transmission that needs study before AMR control Hence, transmission dynamics are important to the programs can be applied on-farm. Drugs critically question of AMR control through animal segregation. important for human medicine are used most Demonstrating common transmission from breeder commonly in people and thus novel resistance flocks to chicks (via the hatchery) or from sows to is most likely to emerge in people. If people suckling pigs before weaning would mean that animal subsequently transmit these resistance elements into flow does not break resistance and an industry-wide otherwise isolated livestock or poultry operations, control effort is needed. Alternatively, rare vertical and amplification, re-assortment, and re-transmission transmission would provide an opportunity for to humans occurs, it exponentially increases the individual operations to address resistance levels. reservoir of resistance. This concern mirrors those These dynamics are likely to be bacterial species- over the role of pigs and poultry in influenza and has specific and are likely to differ between pigs and been demonstrated to occur with methicillin-resistant chickens. In pigs, we would expect that industry-wide Staphylococcus aureus (MRSA) in horses and programs will be needed because piglets are exposed companion animals (184). ‘Humanosis’ control is an to the sow’s feces. understudied area of AMR control. This area of study could be expanded to evaluate the risks of resistant Pigs and chickens can acquire disease from humans. bacteria derived from humans entering barns through To address this risk, visitors may be required to alternative routes, such as water contaminated by have no chicken/pig contact for a certain duration urban effluent (161). before entering the barn (i.e. swine barns often require 48–72 pig-free hours prior to entry). The Biosecurity can be an effective tool to keep herds/ entry requirements for people are more stringent flocks negative for diseases that are enzootic for in breeding flocks/herds than grow-out operations the industry. A study of broiler farms found the because of the continuous presence of valuable odds of being Campylobacter-positive at slaughter

72 national collaborating centre for infectious diseases were nine times higher in control flocks than in and are, to our knowledge, the only national data flocks implementing a biosecurity program. Control describing biosecurity practices in the Canadian flocks were also infected earlier than the ‘biosecure’ swine industry. Biosecurity in American swine herds flocks that broke with disease (521). More research has been described but should not be extrapolated quantifying the effect of biosecurity practices or to Canada as half of the herds reported outdoor systems on animal and zoonotic pathogens is exposure of sows (409). Biosecurity requirements desperately needed. Such work could be expanded to for indoor closed herds differ from free ranging pigs. evaluating associations between biosecurity practices In Canada, maintaining sows outdoors would be a and AMR, as has been done to a degree in studies relatively uncommon practice. Outdoor rearing of that evaluated management practices as risk factors sows would impact sow exposures and disease, thus for AMR in bacteria from healthy pigs (299,516). making any comparisons virtually impossible.

The ‘art’ of biosecurity has traditionally been The swine and broiler industries are embarking on empiric with minimal scientific rigor applied to a new chapter of on-farm programs by developing recommendations (514). Many practices have not on national biosecurity standards. These efforts are been proven to improve productivity or health, and at the conceptual stage but will provide an outlet for despite increased uptake of biosecurity practices in scientific, Canadian-based research. This is a valuable the United States, pig health worsened from 2000 opportunity to investigate potential controls for AMR to 2006 (409). While this may reflect changes in dynamics and transmission. The resultant findings endemic disease or management factors other could be incorporated into these national standards. than biosecurity, it reminds us that biosecurity and Without a concerted effort from researchers and husbandry practices require rigorous scientific scrutiny policy makers, there is a risk that antimicrobial to ensure they actually are an improvement. resistance issues being delegated to one of the many public-good issues will provide insufficient incentive Biosecurity decisions are made on an individual flock/ for producers to act voluntarily. If this is the case, herd basis, and producers implement systems based spin‑off benefits will continue to be the main source on the perceived costs and benefits (522,523). of AMR control in Canadian livestock operations. A variable system places the Canadian livestock industry at risk for foreign animal disease. A review of biosecurity practices in broilers was conducted after Slaughter and Processing the avian influenza outbreaks in British Columbia It is widely held that the best way to mitigate in 2004. Lapses in biosecurity were deemed to foodborne bacterial risk is to reduce the prevalence contribute to disease spread between farms. Data of pathogens in animals pre-harvest (7,455). Yet, do not exist to determine if the practices in British post-harvest interventions have been responsible Columbia are representative of those across Canada for most of the advancements in food-safety from (524). Addressing the reasons for breaches in bacterial disease (321). A growing burden could be biosecurity, along with the reasons for differences placed on the slaughter and processing industries if in biosecurity between flocks, could be relevant producers change AMU practices. Decreased in-feed for understanding what changes are needed in AMU could result in a subsequent decline in carcass biosecurity before programs could consider attempting uniformity, an increase in sub-clinical disease (and to prevent novel resistance elements from becoming therefore more friable intestines), and an increase in established in swine and poultry populations. adhesions from past clinical disease. An increase in these carcass and intestinal characteristics would lead The CIPARS farm swine surveillance collects data to an increased risk of intestinal perforations and fecal describing biosecurity practices on sentinel farms contamination (325,326,525–527), and therefore, a (66). To date, these have not been published reduction in food safety.

www.nccid.ca 73 The meat industries have been proactive in identifying of the advancements in poultry processing is and implementing technologies to control foodborne provided by Bolder et al. (Table 5) (455). Since these bacteria on meat. Interventions have included: interventions control the bacterial host contamination, processes (i.e. separating infected and clean flocks/ they indirectly affect resistance elements on meat herds, application of HACCP systems), physical and control AMR dissemination. Further innovation to interventions (i.e. carcass decontamination with directly address the risk of contamination of carcasses hot water sprays and dips, air chilling, plant design or meat with AMR bacteria currently lacks obvious or to control air flow, automated machine cleaning), simple controls. If the reduction of foodborne AMR and biological and chemical interventions (i.e. bacteria becomes a goal, basic scientific research will bacteriophages to control E. coli O157 on hides, be needed to address this challenge. microbial chemicals) (455,456,528,529). A summary

Table 5. Improvements in poultry processing plants over the past 15 years.

1. Containers have replaced small plastic coops 2. Gas stunning is becoming more popular, with less infection of the air sac, less physical damage to the birds and less defecation while being stunned 3. Counter current and multi-stage scalding systems, where carcasses are washed during scalding 4. Pluckers can be easily turned inside out, allowing cleaning during breaks and more efficient cleaning and disinfection after production, so more efficient hygiene is achievable 5. Re-hanging is fully automated, so cross-contamination during the piling up of carcasses no longer occurs 6. ‘Cleaning In Place’ is installed on modern equipment 7. Modern equipment can be easily adjusted, avoiding damage to intestines from opening machines and during evisceration 8. During carcass opening, a vacuum system removes rectal contents and the cloaca is positioned at the back of the carcass, avoiding contamination of the carcass with intestinal contents 9. At evisceration, intestines are physically separated from the carcasses for inspection 10. Final washing and inspection of carcasses is fully automated and reliable, so no human checks are necessary 11. Air chilling 12. Introduction and application of HACCP 13. Introduction of automatic portioning lines 14. Vision systems introduced 15. Electro-stimulation or maturation at different stages of the process allowing in-line processing including chilling, portioning, and deboning 16. In-line processing with minimal contact between carcasses and with improved tracking and tracing

Reproduced with permission from World’s Poultry Science Association (455).

74 national collaborating centre for infectious diseases Only three aspects of slaughter and meat processing these bacteria could theoretically pass resistance were found that specifically pertained to food safety elements on to commensal or pathogenic bacteria risks from AMR. Interestingly, all were concerns in humans. Although these concerns are theoretical, raised in Europe, and all evaluated the potential for they deserve investigation to determine the likelihood introducing risk rather than risk mitigation. and repercussions of such events.

Microbial control agents (also referred to as Conclusion antimicrobial treatment substances in Europe) are licensed in Canada, the United States, and Australia. This chapter summarized the industry-wide and These include hydrogen peroxide, peroxyacetic acid producer-level activities that reduce the need for (POAA), octanoic acid, peroxyoctanoic acid (POOA), antimicrobials in chickens and pigs. From this and 1-hyroxyethylidene-1, 1-diphosphonic (HEDP) summary, it is evident that the effect of individual acid (528,530). In these countries, microbial control interventions on AMU is unmeasured and a cohesive agents are registered for use on fruits, vegetables, approach is lacking. The two notable gaps in activity meat, and poultry. Most microbial activity is attributed were the lack of education programs on appropriate to POAA with reports of 2- to 9-fold reductions in AMU for producers and animal nutritionists and a lack of publications related to AMR control at slaughter total microbial loads and activity against Listeria and processing. In contrast, the advancements in monocytogenes, E. coli O157 and Salmonella (530). The safety of these compounds was reviewed by animal husbandry, management, and health that the FAO/WHO Expert Joint Committee of Food have occurred concurrently with the intensification of Additives, which ruled that the residual quantities our livestock production have helped to mitigate the of these acids on foods at the time of consumption reliance on antimicrobials that is inherent with large posed no food safety risk (531). In a 2005 report, confinement operations. the European Food Safety Commission echoed this There are two impediments that we believe finding (532), but further assessed the issue in 2007, would speed industry-led action to control AMR if when potential effects on antimicrobial resistance they were removed. The first is a lack of scientific were considered (533). Resistance was defined as evidence regarding the efficacy of interventions. Most both a decreased effectiveness for reducing microbial veterinarians and producers recognize that decreasing load and resistance to therapeutic antimicrobials. AMU is the goal, but the best approach remains The panel concluded that there was no evidence to elusive because rigorously-tested, evidence-based indicate that use will lead to either type of resistance research has largely not occurred. A cohesive industry- but did recommend research on the likelihood of led approach requires a strategy based on science. emergence of resistance (533). Appropriately designed observational studies must The second and third concerns regarding processing be able to attribute AMR changes to an intervention, interventions leading to AMR were summarized by measure confounding effects, evaluate challenges the European Food Safety Authority (106). One and costs that may lead to non-compliance, and concern was that laboratory studies showed that ensure that the AMU alternatives or therapeutic industrial non-thermal processing and preservation drug use shift in response to the intervention are techniques can damage cell membranes, enzymes, beneficial. This is a massive undertaking especially and DNA. This could “promote the generation or since AMR ecology is so complex and to date not transfer of resistance” (106). The other concern was completely understood. However, it is absolutely that bacteria intentionally added to the food chain necessary to begin to take these steps in order to to assist in preservation, or fermentation could serve scientifically address this problem while maintaining a as a source of resistance elements. Much like the viable agriculture industry. concern over commensal bacteria from animals,

www.nccid.ca 75 Economics are the second impediment to industry- led AMR interventions. Producers are financially rewarded for healthy, uniform animals. Antimicrobials currently help to achieve that. Currently, beyond the niche market for antibiotic-free pork/chicken, there are no tangible incentives to offset production risk and losses from interventions to control AMR. At present there are also many industry challenges, such as market access, foreign animal diseases, and extensive financial losses, especially in the pork industry, that are directly jeopardizing producers’ viability. It is very difficult to inspire producers to address AMR issues when their livelihood is threatened. Meat production is how these individuals make their living. Hence, they must see a demonstrable benefit from making changes and implementing new practices, especially to address an issue that is not negatively impacting their production. This would involve producer and industry education, but it would also need to include a component that would help the livestock industry to mitigate risks to animal health, welfare, product quality, and return on investment for making changes to address AMR. Such action is required as incentive to increase the priority of this issue. Widespread industry change will also need innovative ways to ensure cost-sharing between society and industry.

76 national collaborating centre for infectious diseases Chapter 5: Conclusion AMR Bacteria in Agri-food encoded on mobile genetic elements together with other critically important resistance determinants The emergence, dissemination, and maintenance such as extended-spectrum ß-lactamase genes of antimicrobial resistance (AMR) are complex (112,113). If fluoroquinolone resistance is linked to processes that cannot be explained or addressed other resistance genes, then the use of any of the using simplistic methods. Factors such as co-selection linked antimicrobials could increase fluoroquinolone of resistance genes, interactions between bacterial resistance. This emerging issue emphasizes the populations, and variable changes in bacterial fitness need for research into transmission dynamics and after resistance acquisition are but a few complex possible interventions that could prevent human issues that require equally complex investigations AMR problems from becoming established in and interventions. Research regarding AMR must food‑animal populations. be adequately broad to be able to identify true causal relationships. This knowledge can expedite While the potential role of the commensal gut implementing effective interventions and minimize microflora is frequently discussed, investigation of this trial and error in policy changes. diverse and poorly understood bacterial population is quite superficial. A large percentage, if not the Innumerable connections link antimicrobial resistant majority of bacteria present in the intestinal tracts bacteria in humans, food-producing animals, and the of livestock, have likely never been cultured and environment, and believing that we understand all identified. So, current assessments of the commensal of the possible links would be presumptuous. The microflora are presumably being based on a small, transmission rates for these links are unknown, but and not necessarily representative, component of the food is a universal and direct connection between bacterial population. Considering that this bacterial people and animals. It is irrefutable that people population may be of greater relevance to AMR can acquire antimicrobial resistant bacteria from than pathogenic bacteria, greater study, in quantity animals through food. What remains disputed is the and depth, of the commensal microflora is required. frequency that pathogenic and commensal bacteria This should include broader study of the true nature are transmitted to humans and either cause disease of the microflora, the effects of antimicrobial use or transfer resistance elements to bacteria in people. (AMU) on population dynamics and on AMR, and the A related knowledge gap is the relative amounts interaction between the commensal microflora and that AMU in animals and humans each contribute to pathogens. Furthermore, more research is needed AMR in humans. Answers to these questions would on environmental bacteria to investigate connections allow policy makers to evaluate the magnitude of between AMR in soil bacteria and human commensal risk imposed on the population by contaminated and pathogenic bacteria (534). Our limited food and would allow appropriately aggressive understanding of commensal bacterial ecology is intervention strategies. illustrated by the much studied relationship between Resistant pathogenic bacteria are the most obvious E. faecium in livestock and people. This commensal food safety concern. Within these bacteria, new bacterium is ubiquitous in humans, swine, and threats are constantly emerging, such as the novel poultry. But determining the extent to which these plasmid-mediated fluoroquinolone resistance bacterial populations are host adapted, interact, and genes. It is likely, and perhaps even inevitable, share resistance elements has challenged the limits that fluoroquinolone resistance genes will become of science (156,159–161). Molecular epidemiology established in commensal and pathogenic bacteria is constantly responding to this and similar challenges in swine and poultry (74,107). Equally concerning through new tools. Ultimately, we hope this will is the potential for fluoroquinolone resistance to be enable scientists to quantify these relationships, which

www.nccid.ca 77 would allow interventions to focus on the greatest understanding of AMU and AMR is required. If this risks to human health. field is to truly develop, new methodologies and populations need to be used, and better collaboration The public health community has seen resistant between the fields of epidemiology, microbiology, nosocomial pathogens expand their niche into molecular biology, ecology, food safety, and animal communities. Concurrently, health and veterinary management are required. This type of integrated authorities are acknowledging the porousity of study can be technically challenging and expensive, the human/animal boundary to many bacteria. but has great potential to generate true and accurate Controlling the ‘infectious traffic’ between nosocomial, understanding of causal determinants of AMR. community and animal bacterial populations will Funding agencies need to be open to supporting be an increasingly important task for AMR control. broader and novel methods as, in the long run, these Future challenges are highly unpredictable, as already may be a more efficient use of resources. demonstrated by the potential for methicillin-resistant S. aureus (MRSA) and C. difficile to be zoonotic. The Active research is exponentially increasing the identification of MRSA in food animals and food has information available about AMR in food animals. raised concerns about the risk of foodborne human Each study adds a piece to the puzzle. But the MRSA infection (202–207). Basic food handling and sheer volume of scientific publications is becoming cooking practices should greatly reduce the risk of unwieldy and is presenting challenges for concise food acting as a mode of transmission, but the risks and current knowledge translation to researchers cannot (and should not) be assumed to be negligible and practitioners who need to apply these findings. in the absence of evidence. More intensive research We face the risk of data overload, where policy and in this field is required, particularly characterization practice is unable to assimilate new advancements of strains found in pigs in Canada, mechanisms and contextualize novel discoveries. The rapid of foodborne contamination, and epidemiological expansion of information, often with conflicting investigation of food contact as a risk factor for results, means literature reviews quickly become community-associated MRSA infection in people. obsolete and are prone to biased interpretations. In Clostridium difficile is also a high profile pathogen the health sciences, meta-analyses and systematic with recent concerns about foodborne transmission reviews are used to compile multiple research (225,241,242). The role of food in human C. difficile findings. These techniques can evaluate specific and infection is unclear and is coupled with a rather extensively-studied questions, but are insufficient for superficial understanding of the role ofC. difficile understanding and communicating knowledge on in community-onset diarrhea in humans. Study of many issues because the topic and concerns with the role of C. difficile in community-onset diarrhea AMR are broad, and understanding of diverse but and food as a risk factor for community-associated inter-related aspects is necessary. Yet, we believe C. difficile infection is needed. that analogous approaches must be developed through multidisciplinary teams involving information Despite the abundance of data regarding AMR technology specialists, librarians, and scientists to and livestock, some significant deficiencies exist. assimilate the vast scope of AMR knowledge and While large volumes of data are present, there is reliably evaluate conflicting findings. Without such tremendous repetition of the same methodologies tools, information paralysis may undermine the value in the same regions or between regions. This can of current and future research. In a related vein, provide information about inter or intra-region decision analyses have been used to model health differences or changes, but it can also result in decisions at individual and population levels. We generation of data that contribute little to the suggest it would be useful to investigate whether overall understanding of AMR and AMU. While similar techniques could assist in incorporating new continuation of such studies is relatively easy, information into intervention or policy decisions. expansion of research to encompass a broader

78 national collaborating centre for infectious diseases Antimicrobial use in Food Animals increasing AMU are stronger and more consistent than studies showing a decrease in AMR following Antimicrobials are used in food-animal production withdrawal of AMU. Declining resistance after around the world. The food safety hazards arising drug cessation has been demonstrated for some from this vary based on the types and amounts pathogen/drug combinations, but it is certainly not of antimicrobials used. But despite the concerns universal and has often been less substantial and about AMU on farms and the interventions that are sustained than was expected. This is important recommended or implemented, our understanding because it suggests that established AMR is not of AMU practices remains limited. This is problematic consistently resolved by removing the inciting cause. because assumptions and weak data are being used Our ability to contain or decrease specific AMR trends to determine policy, strategy, and even legislation. may be limited. Many factors, including co‑selection, Antimicrobial volumes collected through sales bacterial fitness, and linkages with virulence and other data may be reliable, but are of limited value by important genes, means that a direct relationship themselves for understanding AMR. Many products between AMU and AMR is not always present. are licensed in numerous species for multiple Therefore, efforts focused simply on one organism indications and may also be used in an extra-label or one antimicrobial could be inadequate. Research manner. Antimicrobial volumes cannot reflect demonstrating the effectiveness of a variety of selective pressure without accounting for the recipient interventions to mitigate existing AMR, only one of population (535). In contrast, end-user data hold which should be drug withdrawal, will be necessary great potential for identifying risk factors for AMR for future policy. This should include interventions but are more prone to bias and are more costly to through sanitation, animal movement, and husbandry. collect. We have seen global progress in standardizing antimicrobial susceptibility testing and surveillance The apparent relationship between in ovo ceftiofur techniques (281,408). Ideally, advancements in AMU use and resistance in human Salmonella isolates data collection will soon follow. This will allow for valid illustrates how agricultural AMU can affect humans. analysis of the selective pressures for resistance and The correlation between decreasing AMR in will bolster the validity of ecological level studies. Salmonella and E. coli from chicken following reports of voluntary cessation of the practice and return In the meantime, it is widely stated that antimicrobials of resistance after use was reportedly reinstituted are necessary for animal health and welfare. We are one of the clearest demonstrations of the link agree that AMU is vital for humane animal production between AMU and AMR (117). However, these but AMU can also compensate for sub-optimal surveillance findings need additional research to management. The true role of antimicrobials in clarify the total effect of AMR/AMU interventions on animal health and welfare needs to be objectively human health. For example, research is needed on quantified. The AMU that is unnecessary or human health repercussions from the rise in ESBL unreasonable must be eliminated while preserving resistant E. coli in chicken that paralleled the rise in use that is required to produce safe food, humanely Salmonella Heidelberg (Chapter 2; Figure 2). Food rear livestock, and ensure economic viability of safety research is also needed, such as comparing the industry. Research should broadly consider pathogen loads on the carcasses derived from treated animal health, economics, and AMR. Answering and untreated eggs, and comparing the health and these questions could be facilitated by evaluating subsequent AMU in chicks that did and did not differences between conventional, antibiotic-free, and receive ceftiofur in ovo. Surveillance should be used organic production systems. as a time sensitive tool to instigate research activities It was traditionally believed that ceasing AMU that expand beyond the farm-to-fork continuum to would inevitably and promptly lead to reductions in measure a wide range of effects on human health. AMR. But data supporting an increase in AMR with

www.nccid.ca 79 Quantitative risk assessments have examined the International standards, such as the draft methods magnitude of risk imposed on people from foodborne released by Codex to conduct risk assessment, resistant bacteria. Several American publications can help to smooth trade but are not enforceable estimated substantially lower risks than were intuitive regulations (536–538). Thus, member countries can based on a qualitative evaluation of the literature still set their own requirements. For example, risk (8,85,526). These models can provide a tool to prioritization relies on the ranking of antimicrobials for investigate the relative importance of transmission their importance to human medicine. But countries pathways, but are limited in scope to known and may rank antimicrobials using a list developed studied connections. Therefore, our confidence in the through international consensus or one reflecting the input parameters determines their validity. To date, concerns of the member country (86,388). Trade quantitative risk assessments have been confined to barriers to control animal or foodborne resistant single pathogen/antimicrobial combinations. Perhaps bacteria have not yet occurred but are a realistic in the future it will be possible to expand the scope concern given the increasing divergence in regulations of risk assessments to account for a wide variety of and controls between countries. Until such a barrier repercussions including environmental contamination is invoked, challenged, and ruled on by the World from AMU, environmental pollution from lack of AMU, Trade Organization, the ability of countries to block animal health and carcass characteristics, pathogen importation of products based on antimicrobial use or loads on meat, and nutritional repercussion from resistance remains speculative. changing meat prices. This would be a colossal undertaking but would help ensure policy results in Canada has played an active international role in AMR the greatest benefits for society. policy. We applaud the efforts to support evidence- based regulations. It is important that Canada Legislation, Regulation, and Policy continue to push other nations to address high-risk to Address Antimicrobial Resistance drug use practices because the problem of AMR is truly global. Movement of animals, people, and in Agri-Food food means that Canadians are affected by AMR in The WHO, OIE, and FAO have led international distant countries. The Canadian government also has co‑operation to address foodborne resistant bacteria. a responsibility to the agriculture sector to hold our These agencies have released prudent use guidelines competitors to similar standards as are imposed at and collaborated on risk assessment techniques. home. Much remains to be achieved on this front as The effects of these actions on AMU and AMR many competitors have permissive veterinary drug are difficult to judge because countries that have regulations and scant to non-existent reporting. The implemented regulations and policies may have done reverse of this statement is also true. Canada has so in the absence of these mandates, while others more permissive veterinary drug regulations than may be preparing to act but appear unresponsive. Europe or the United States. If we expect to hold Some of the countries that have not developed other countries accountable to our standards, we formalized systems to address AMR have either will be expected to respond to the concerns raised piloted surveillance programs or conducted research over our inability to ensure prudent antimicrobial use into AMR in foodborne bacteria. This indicates that (248,385). concern is widespread. Canada is one of several countries that has National differences in veterinary drug regulations established an agri-food AMR surveillance system. and AMU/AMR monitoring raise concerns about Amongst these, Canada stands out as one of the the international movement of animals and food. most comprehensive. Unlike many other programs, Importing nations are concerned about the safety Canada monitors three steps of the production of imported products and exporting nations are chain—the farm, abattoir, and retail—and annually concerned about open and transparent trade. collects samples for a range of bacteria in every

80 national collaborating centre for infectious diseases major food commodity (66). Advancements in recommend the VDD commit to evaluating policy collecting AMU data from pigs, with parallel initiatives for efficacy with established targets to ensure it is in other commodities, have made this a robust and working. In the case of ineffectiveness or (even comprehensive program. From the swine component, worse) harm, the VDD must be committed to positive news has emerged including the absence revoking or changing such policy. We urge the VDD of fluoroquinolone use and close to 10% of sentinel to work in conjunction with the appropriate provincial farms voluntarily using no antimicrobials. Concerning regulators to address the thoroughly investigated practices have also been identified including ceftiofur recommendations of the 2002 Advisory Committee use and long-term macrolide use. The swine and on Animal Uses of Antimicrobials and Impact broiler industries have recognized the value of on Resistance in Human Health before they are third‑party reporting to demonstrate transparency. obsolete (248). Ideally, this system should enhance the effectiveness of policy addressing AMU in Canada. Agri-food Industry Actions to Address AMR Collecting multi-source AMR data allow ‘farm-to‑fork’ risks to be studied. We recommend continued The broiler, swine, veterinary, and meat industries strengthening of the CIPARS program design to draw continue to make advancements that improve causal links from AMU in animals to AMR in animals animal health and decrease their reliance on to AMR in humans. Surveillance programs are most AMU. Excluding the prudent AMU guidelines for effective when the data collected are consistent veterinarians, these actions are not undertaken over time. Canada has developed a comprehensive specifically to address AMU and so their effects on program, but due to budgetary limitations, there are AMR are presumed but unconfirmed. Viable on-farm some concerns about long-term sustainability of food safety (OFFS) programs in the chicken and the farm component in its current form. Continued pork sectors are consistently implemented across research into alternative AMU data collection Canada (284,458). When sufficient knowledge methods, such as surveys and data extrapolation, pertaining to on-farm AMR is available, these could may identify valid and cost-effective alternatives. provide a foundation for creating and delivering an Preparing for the worst is an unfortunate reality of AMR control program. Beyond these, we have limited shifting budget priorities. However, we advocate knowledge of how extensively the other activities are continued support for Canada’s CIPARS program and used across the industry. Prudent AMU guidelines its expansion to other provinces and commodities. were the only identified activity that specifically addresses AMR. These guidelines tend to be broad- The Canadian regulatory system is committed based and provide little clear information about how to evidence-based policy. This has led to risk to incorporate prudent use into current practices assessments being applied to new drug applications (395). Of the numerous guidelines that exist, we and potentially to future post-approval evaluations. found none that were monitoring their influence on Canada has been criticized for its veterinary drug AMU. This information void is unfortunate because, regulations by national and international experts. without evidence of their effect, it is difficult to Clearly, the VDD acknowledges these criticisms sustain the necessary funding to promote, update, and is striving to address them as shown by the and modify the standards in order to keep them extensive stakeholder consultations that have viable. Also it is impossible to identify the ineffective occurred since 2002 (285,364,391,394). From areas for improvement. The Canadian Veterinary an outside perspective, it appears that stakeholder Medical Association (CVMA) generated the most paralysis may be an issue. This will be challenging recent guidelines for Canadian swine and poultry for the VDD to address, as science will not be able veterinarians (390). We urge the CVMA to survey to provide definitive solutions to many of the current its membership on AMU practices and attitudes concerns before regulatory changes are needed. We immediately to provide a baseline for the recently

www.nccid.ca 81 released guidelines, with follow-up surveys on the repeated introduction of bills that threaten to revoke use of these guidelines. Compared to the efforts that antimicrobials, which has fostered distrust, fear, and have gone into the creation of this document, this non-cooperation between corporate agriculture and seems like a small and invaluable undertaking. In health activists. Canada should strive for an innovative conjunction, we support a collaborative relationship and collaborative relationship between the medical, between the CVMA, the Chicken Farmers of Canada veterinary, and agriculture communities. If public (CFC), the Canadian Pork Council (CPC), and the health authorities explored the risks of inaction in Animal Nutrition Association of Canada (ANAC) conjunction with the agriculture industry, and funding to develop and deliver prudent use education for agencies concurrently provided resources for applied producers and animal nutritionists. These groups are innovations, while regulators minimized impediments the greatest users of non-prescription antimicrobials, to novel alternatives, we could collectively enable the thus this may counterbalance Canada’s controversial agriculture industry to drive, rather than drag, solutions regulations. Data describing how and why producers for AMU and AMR. make AMU decisions exist but have not been utilized. This could strengthen the creation of prudent use Main Recommendations and programs for producers and shape effective policy. Thus, our final recommendation to the CFC and Knowledge Needs CPC is to analyze and disseminate the valuable • Initiate investigations into techniques for knowledge information they possess describing AMU attitudes, assimilation, evaluation, and utilization OFFS program sustainability, and the implementation of best management practices. • Seek and support research into the effectiveness of interventions, including but not limited to AMU Vaccines, competitive exclusion strategies, nutritional withdrawal, to mitigate existing AMR and apply such advancements, and biosecurity were presented as findings to future policies and actions examples of industry-led advancements to decrease reliance on antimicrobials. Research to develop new • Seek and support innovative research that expands products and to identify new biosecurity techniques on the current ‘farm-to-fork’ approach to truly will continue to improve animal health. Indirect account for diverse human health outcomes support for prudent AMU must not be undervalued. • Continue to advocate for fair, transparent, veterinary Funding agencies should continue to invest in health- drug regulations, AMR and AMU monitoring building research. Data on the extent that these around the world based on scientific evidence, risk alternative management practices are implemented assessment, and appropriate precaution to ensure nationally, and their alleviation of AMU dependence, free and open trade of safe meat products could be studied. • Change Canada’s veterinary drug regulations Empirically, it appears that the implementation of to ensure prudent and safe antimicrobial use interventions by industry correlates with financial in animals and commit to transparent policy reward and/or risk mitigation. Perhaps Canada’s evaluation and action in the absence of efficacy or public health and agriculture sectors can learn demonstrable harm from two recent American experiences. A positive example was set when the United States’ Waxman- • Deliver antimicrobial use education to producers Markey clean energy bill was strongly supported by and nutritionists corporate America because it fostered innovation in the corporate sector without stifling financial • Foster an innovative and collaborative relationship gain from innovation and early adoption (539). In between regulators, public health officials and the contrast, a negative example has been set by the agriculture industry

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110 national collaborating centre for infectious diseases Appendix 1: Search Strategy

The following search terms and combinations of key MeSH terms, truncation, and Boolean operaters words were provided to the librarian. These were were used at the librarian’s discretion. Additional used, along with her expert knowledge regarding consultation between the librarian and team database capabilities and medical subject headings members occurred to identify inclusion criteria with (MeSH), to conduct the systematic searches of CAB, incomplete/insufficient citations identified, and ad hoc EMBASE, and Medline, and the strategic searches of searches were conducted but not recorded. Scopus and Agricola. Searches were generally limited to the word being in the title, original title, abstract, The search results were downloaded into name of substance word, subject heading word, RefWorks ©. Duplicates were automatically removed or unique identifier. An English language restriction thus the numbers of citations obtained prior to and publication date restrictions were used (First removing duplicates are not available. set; 1990 to present; Second set; 1999 to present).

Database Citations obtaineda Embase/Medlineb 1524 CAB 485 Scopus 114 Agricola Not recorded a The citations obtained refers to unique citations after duplicates were automatically removed. b Embase and Medline were combined due to high degree of overlap.

www.nccid.ca 111 Search Number Search Terms 1.1 E* coli or Esherichia coli 1.2 Campylobact* OR C* coli OR C* jejuni 1.3 Salmonell* NOT Typhi 1.4 Enterococc* OR VRE OR (vancomycin NEAR Enterococc*) 1.5 Clostridi* AND (difficile OR perfringens) 1.6 Yersini* 1.7 MRSA OR (Staph* AND aureus AND methicillin) 1.8 Lact* AND bacteria 1.9 Listeri* 1 COMBINE TO MAKE SET #1 2.1 Poult* OR Chicken OR Broiler OR breeder OR Hatch* NOT (egg OR turkey OR layer) 2.2 Swine OR pig OR porcine 2.3 Food* OR Meat OR agri* OR muscle AND (Chicken OR Pork) NOT (beef) 2.4 2.3 AND (consumption OR handl*) 2.5 2.1 or 2.2 AND (fecal or feces or ceacal or cecal) 2 COMBINE TO MAKE SET #2 3.1 Anti* NEAR (bacterial OR biotic OR microb* OR drug) 3.2 3.1 NEAR (resist* OR suscept* OR sensitiv*) 3.3 3.1 AND Class NEAR (rank OR classification OR order OR importance) 3.4 ionophore OR “feed additive” OR “feed antibiotic” therapeutic or *drug or drug* 3 COMBINE TO MAKE SET #3 4.1 1 OR 2 OR 3 NEAR (control OR interven* OR prevent* OR transmi* OR monitor OR surveil*) 4.2 1 OR 2 OR 3 NEAR (policy OR protocol OR action OR program OR strategy OR position) 4.3 1 OR 2 OR 3 NEAR (guidelines OR “best practice” OR regulat* OR legislat* OR legal) 4.4 1 OR 2 OR 3 NEAR (good NEAR management OR production) 4.5 1 OR 2 OR 3 NEAR (“critical control point” OR “standard operating” OR HACCP) 4.6 1 OR 2 OR 3 NEAR (monitor* OR surveillance OR “public health” OR stewardship)

112 national collaborating centre for infectious diseases 5.1 2 NEAR (Industry OR produce* OR farm* OR process* OR Abattoir OR Distribut* OR commodity) 5.2 (govern* OR regulat*) NEAR (health OR agri*) 5.3 5.2 AND (Canada OR United States OR US* OR Mexico) 5.4 5.2 AND (Europ* OR “South America” OR … specific inclusion criteria 5.5 (Vet* OR Practition*) AND (Association OR Organization) 5.6 2 AND pharmaceutical 6.1 2 and 5 (best if includes 1 or 4) AND nutri* OR feed 6.2 2 and 5 (best if includes 1 or 4) AND feed NEAR (probiotic OR prebiotic OR “essential oil” OR herd OR alternative) 6.3 2 and 5 (best if includes 1 or 4) AND organic OR (anti* NEAR free) 6.4 2 and 5 (best if includes 1 or 4) AND biosecurity OR (wash OR “down time” or boot OR fly OR shower) 6.5 2 and 5 (best if includes 1 or 4) NEAR (disease OR health) 6.6 2 and 5 (best if includes 1 or 4) AND hygiene OR disinfect* OR detergent OR sanitation OR wash OR dry 6.7 2 and 5 (best if includes 1 or 4) AND batch OR (all NEAR in) 6.8 2 and 5 (best if includes 1 or 4) AND dead OR cull OR compost OR mortality OR condemn* OR render 6.9 2 and 5 (best if includes 1 or 4) AND morbidity OR sick OR treatment 7.0 2 and 5 (best if includes 1 or 4) AND (medication OR vaccine OR drug) NEAR (storage OR handling OR use) 7.1 2 and 5 (best if includes 1 or 4) AND (air NEAR ventilation OR quality OR gas OR humidity OR flow OR ammonia) 7.2 2 and 5 (best if includes 1 or 4) AND (water NEAR pipes OR biofilm OR quality OR chlorin*) 7.3 2 and 5 (best if includes 1 or 4) AND ship* OR transport* OR handl* OR lairage 7.4 2 and 5 (best if includes 1 or 4) AND litter 7.5 2 and 5 (best if includes 1 or 4) AND brooding 7.6 2 and 5 (best if includes 1 or 4) AND bacteria AND (preservative OR *radiat* OR wash OR bacteriocin OR lactibiotic OR bacteriophage) 7.7 3 and 5 (best if includes 1 or 4) AND bacteria AND (chill OR steam OR OR packag*)

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